aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets
Version 3.1.0

A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.

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AuthorHenrik Bengtsson [aut, cre, cph], James Bullard [ctb], Kasper Hansen [ctb], Pierre Neuvial [ctb], Elizabeth Purdom [ctb], Mark Robinson [ctb], Ken Simpson [ctb]
Bioconductor views CopyNumberVariants DataImport DataRepresentation DifferentialExpression ExonArray GUI GeneExpression Infrastructure Microarray OneChannel Preprocessing ProprietaryPlatforms QualityControl ReportWriting SNP Transcription Visualization aCGH
Date of publication2017-03-24 05:36:49 UTC
MaintainerHenrik Bengtsson <henrikb@braju.com>
LicenseLGPL (>= 2.1)
Version3.1.0
URL http://www.aroma-project.org/ https://github.com/HenrikBengtsson/aroma.affymetrix
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("aroma.affymetrix")

Man pages

AbstractProbeSequenceNormalization: The AbstractProbeSequenceNormalization class
AdditiveCovariatesNormalization: The AdditiveCovariatesNormalization class
AffineCnPlm: The AffineCnPlm class
AffinePlm: The AffinePlm class
AffineSnpPlm: The AffineSnpPlm class
AffymetrixCdfFile: The AffymetrixCdfFile class
AffymetrixCelFile: The AffymetrixCelFile class
AffymetrixCelSet: The AffymetrixCelSet class
AffymetrixCelSetReporter: The AffymetrixCelSetReporter class
AffymetrixCelSetTuple: The AffymetrixCelSetTuple class
AffymetrixCnChpSet: The AffymetrixCnChpSet class
AffymetrixFile: The abstract AffymetrixFile class
AffymetrixFileSet: The AffymetrixFileSet class
AffymetrixFileSetReporter: The AffymetrixFileSetReporter class
AffymetrixPgfFile: The AffymetrixPgfFile class
AffymetrixProbeTabFile: The AffymetrixProbeTabFile class
AlleleSummation: The AlleleSummation class
AllelicCrosstalkCalibration: The AllelicCrosstalkCalibration class
allocateFromCdf.AffymetrixCelFile: Creates an empty CEL file from a template CDF
allocateFromCdf.AromaUnitTabularBinaryFile: Creates an AromaUnitTabularBinaryFile mapping to a given CDF
aroma.affymetrix-package: Package aroma.affymetrix
AromaChipTypeAnnotationFile: The AromaChipTypeAnnotationFile class
ArrayExplorer: The ArrayExplorer class
as.AffymetrixCelSet.AffymetrixCelSet: Coerce an object to an AffymetrixCelSet object
as.AffymetrixCnChpSet.AffymetrixCnChpSet: Coerce an object to an AffymetrixCnChpSet object
as.AffymetrixFileSet.AffymetrixFileSet: Coerce an object to an AffymetrixFileSet object
as.character.AffymetrixCelSet: Returns a short string describing the Affymetrix CEL set
as.character.AffymetrixCnChpSet: Returns a short string describing the set
as.character.CnagCfhSet: Returns a short string describing the CNAG CFH set
as.character.DChipDcpSet: Returns a short string describing the DChip CHP set
as.CnagCfhSet.CnagCfhSet: Coerce an object to an CnagCfhSet object
as.DChipDcpSet.DChipDcpSet: Coerce an object to an DChipDcpSet object
averageQuantile.AffymetrixCelSet: Calculates the average empirical distribution across all...
AvgCnPlm: The AvgCnPlm class
AvgPlm: The AvgPlm class
AvgSnpPlm: The AvgSnpPlm class
BackgroundCorrection: The BackgroundCorrection class
BaseCountNormalization: The BaseCountNormalization class
BasePositionNormalization: The BasePositionNormalization class
bpmapCluster2Cdf: Creates a CDF from tiling-array BPMAP file
byChipType.AromaChipTypeAnnotationFile: Defines an AromaChipTypeAnnotationFile object by chip type
byChipType.DChipGenomeInformation: Defines a DChipGenomeInformation object by chip type
byChipType.DChipSnpInformation: Defines a DChipSnpInformation object by chip type
byChipType.GenomeInformation: Static method to define a genome information set by chip type
byChipType.SnpInformation: Static method to define a genome information set by chip type
byChipType.UgpGenomeInformation: Defines a UgpGenomeInformation object by chip type
byPath.AffymetrixFileSet: Defines an AffymetrixFileSet object by searching for...
calculateBaseline.ChipEffectSet: Estimates the baseline signal chromosome by chromosome
calculateParametersGsb.AffymetrixCelSet: Computes parameters for adjustment of specific binding
calculateResidualSet.FirmaModel: Gets the set of residuals corresponding to the PLM
ChipEffectFile: The ChipEffectFile class
ChipEffectGroupMerge: The ChipEffectGroupMerge class
ChipEffectSet: The ChipEffectSet class
ChipEffectTransform: The ChipEffectTransform class
clearData.AffymetrixCelFile: Clears all or a subset of the fields in a CEL file
CnagCfhFile: The CnagCfhFile class
CnagCfhSet: The CnagCfhSet class
CnChipEffectFile: The CnChipEffectFile class
CnChipEffectSet: The CnChipEffectSet class
CnPlm: The CnPlm class
CnProbeAffinityFile: The CnProbeAffinityFile class
compare.AffymetrixCdfFile: Checks if two AffymetrixCdfFile objects are equal
computeAffinities.AffymetrixCdfFile: Calculates probe affinities from sequence
convert.AffymetrixCdfFile: Converts a CDF into the same CDF but with another format
convertUnits.AffymetrixCdfFile: Gets and validates unit indices
createExonByTranscriptCdf.AffymetrixCdfFile: Creates an exon-by-transcript CDF
createFrom.AffymetrixCelFile: Creates a CEL file using another as a template
createMonocellCdf.AffymetrixCdfFile: Creates a mono-cell version of the CDF
createUniqueCdf.AffymetrixCdfFile: Creates a unique-cell version of the CDF
CrlmmParametersFile: The CrlmmParametersFile class
CrlmmParametersSet: The CrlmmParametersSet class
DChipCdfBinFile: The DChipCdfBinFile class
DChipDcpFile: The DChipDcpFile class
DChipDcpSet: The DChipDcpSet class
DChipGenomeInformation: The DChipGenomeInformation class
DChipQuantileNormalization: The DChipQuantileNormalization class
DChipSnpInformation: The DChipSnpInformation class
doCRMAv1: Estimation and assessment of raw copy numbers at the single...
doCRMAv2: A single-array preprocessing method for estimating...
doFIRMA: Finding Isoforms using Robust Multichip Analysis (FIRMA)
doGCRMA: Robust Multichip Analysis (GCRMA)
doRMA: Robust Multichip Analysis (RMA)
ExonChipEffectFile: The ExonChipEffectFile class
ExonChipEffectSet: The ExonChipEffectSet class
ExonProbeAffinityFile: The ExonProbeAffinityFile class
ExonRmaPlm: The ExonRmaPlm class
extractAffyBatch.AffymetrixCelSet: Extracts an in-memory AffyBatch object from the CEL set
extractDataFrame.ParameterCelSet: Extract data as a data.frame for a set of arrays
extractExpressionSet.ChipEffectSet: Extracts an in-memory ExpressionSet object
extractFeatureSet.AffymetrixCelSet: Extracts CEL signals an in-memory FeatureSet object
extractMatrix.AffymetrixCelSet: Extract data as a matrix for a set of arrays
extractMatrix.ParameterCelSet: Extract data as a matrix for a set of arrays
findByChipType.AffymetrixCdfFile: Locates a CDF file from its chip type
findByChipType.AffymetrixPgfFile: Locates a PGF file from its chip type
findByChipType.AromaChipTypeAnnotationFile: Locates an annotation file by its chip type
findUnitsTodo.FirmaModel: Identifies non-fitted units
findUnitsTodo.ProbeLevelModel: Identifies non-fitted units
findUnitsTodo.UnitModel: Identifies non-fitted units
FirmaFile: The FirmaFile class
FirmaModel: The FirmaModel class
FirmaSet: The FirmaSet class
fit.FirmaModel: Estimates the model parameters
fit.Model: Estimates the model parameters
fit.ProbeLevelModel: Estimates the model parameters
fitQuantileNormFcn.AffymetrixCelFile: Fits quantile normalization functions for the arrays in the...
fit.SingleArrayUnitModel: Estimates the model parameters
fit.SmoothMultiarrayModel: Fits the model for one chromosome across samples
FragmentEquivalentClassNormalization: The FragmentEquivalentClassNormalization class
FragmentLengthNormalization: The FragmentLengthNormalization class
fromCdf.GenomeInformation: Static method to define a genome information set from a CDF
fromCdf.SnpInformation: Static method to define a genome information set from a CDF
fromDataFile.ChipEffectFile: Retrive an existing CEL file, or create from CDF template if...
fromFile.AffymetrixCdfFile: Defines an AffymetrixCdfFile object from a CDF file
fromFile.AffymetrixCelFile: Defines an AffymetrixCelFile object from a CEL file
fromFile.AffymetrixPgfFile: Defines an AffymetrixPgfFile object from a PGF file
fromFile.AromaChipTypeAnnotationFile: Sets up an AromaChipTypeAnnotationFile
fromFile.CnagCfhFile: Defines an CnagCfhFile object from a CFH file
GcContentNormalization: The GcContentNormalization class
GcContentNormalization2: The GcContentNormalization2 class
GcRmaBackgroundCorrection: The GcRmaBackgroundCorrection class
GenericReporter: The GenericReporter class
GenomeInformation: The GenomeInformation class
getAlias.GenericReporter: Gets the alias of the report
getAlias.Model: Gets the name alias for the model
getAlleleCellPairs.AffymetrixCdfFile: Gets the cell indices of allele pairs
getAlleleProbePairs3.AffymetrixCdfFile: Gets the indices of probepairs with the same pair of SNP...
getAlleleProbePairs.AffymetrixCdfFile: Gets the indices of probepairs with the same pair of SNP...
getAM.ChipEffectFile: Gets the log-intensities and log-ratios of chip effects for...
getAM.ChipEffectSet: Gets the log-intensities and log-ratios of chip effects of...
getAverageFile.AffymetrixCelSet: Calculates the mean and the standard deviation of the cell...
getAverageFile.CnagCfhSet: Calculates the mean and the standard deviation of the cell...
getBaseline.ChipEffectSet: Gets the baseline signals across chromosomes
getCdf.AffymetrixCelFile: Gets the CDF structure for this CEL file
getCdf.AffymetrixCelSet: Gets the CDF structure for this CEL set
getCdf.CnagCfhFile: Gets the CDF structure for this CEL file
getCdf.CnagCfhSet: Gets the CDF structure for this CFH set
getCdf.Model: Gets the CDF structure for this model
getCellIndices.AffymetrixCdfFile: Gets the cell indices unit by unit
getCellIndices.ChipEffectFile: Retrieves tree list of cell indices for a set of units
getCellIndices.CnChipEffectFile: Retrieves tree list of cell indices for a set of units
getCellIndices.CnProbeAffinityFile: Retrieves tree list of cell indices for a set of units
getCellIndices.ExonChipEffectFile: Retrieves tree list of cell indices for a set of units
getCellIndices.ExonProbeAffinityFile: Retrieves tree list of cell indices for a set of units
getCellIndices.FirmaFile: Retrieves tree list of cell indices for a set of units
getCellIndices.ProbeAffinityFile: Retrieves tree list of cell indices for a set of units
getCellIndices.ResidualFile: Retrieves tree list of cell indices for a set of units
getCellIndices.SnpChipEffectFile: Retrieves tree list of cell indices for a set of units
getCellIndices.SnpProbeAffinityFile: Retrieves tree list of cell indices for a set of units
getCellIndices.UnitModel: Gets the cell indices unit by unit
getCellIndices.WeightsFile: Retrieves tree list of cell indices for a set of units
getChipEffectSet.AlleleSummation: Gets the set of chip effects for this model
getChipEffectSet.ProbeLevelModel: Gets the set of chip effects for this model
getChipType.AffymetrixCelFile: Gets the chip type for this CEL file
getChipType.AffymetrixCelSet: Gets the chip type for this CEL set
getChipType.CnagCfhFile: Gets the chip type for this CEL file
getChipType.GenomeInformation: Gets the chip type of this genome information set
getChipType.SnpInformation: Gets the chip type of this genome information set
getCnNames.AffymetrixCdfFile: Gets the names of the CN units
getData.GenomeInformation: Gets all or a subset of the genome information data
getDataSet.AffymetrixCelSetReporter: Gets the data set
getDataSet.ArrayExplorer: Gets the data set
getDataSet.Model: Gets the input data set for this model
getData.SnpInformation: Gets all or a subset of the genome information data
getFirmaSet.FirmaModel: Gets the set of FIRMA results for this model
getFitUnitGroupFunction.AffinePlm: Gets the low-level function that fits the PLM
getFitUnitGroupFunction.AvgPlm: Gets the low-level function that fits the PLM
getFitUnitGroupFunction.ExonRmaPlm: Gets the low-level function that fits the Exon PLM
getFitUnitGroupFunction.FirmaModel: Static method to get the low-level function that fits the PLM
getFitUnitGroupFunction.HetLogAddPlm: Gets the low-level function that fits the PLM
getFitUnitGroupFunction.MbeiPlm: Gets the low-level function that fits the PLM
getFitUnitGroupFunction.MultiArrayUnitModel: Static method to get the low-level function that fits the PLM
getFitUnitGroupFunction.RmaPlm: Gets the low-level function that fits the PLM
getFitUnitGroupFunction.SingleArrayUnitModel: Static method to get the low-level function that fits the PLM
getFullName.Model: Gets the full name of the output set
getFullName.TransformReport: Gets the full name of the output data set
getGenomeInformation.AffymetrixCdfFile: Gets genome information for this chip type
getHeader.AffymetrixCdfFile: Gets the header of the CDF file
getHeader.AffymetrixCelFile: Gets the header of the CEL file
getHeader.AffymetrixPgfFile: Gets the header of the PGF file
getHeader.AromaChipTypeAnnotationFile: Gets the header of the annotation file
getHeader.CnagCfhFile: Gets the header of the CEL file
getImage.AffymetrixCelFile: Creates an RGB Image object from a CEL file
getInputDataSet.TransformReport: Gets the source data set
getIntensities.AffymetrixCelSet: Gets cell intensities from a set of cells and a set of arrays
getName.GenericReporter: Gets the name of the explorer
getName.Model: Gets the name of the output data set
getName.TransformReport: Gets the name of the output data set
getOutputDataSet.Transform: Gets the transformed data set
getOutputDataSet.TransformReport: Gets the transformed data set
getPath.Model: Gets the path of this model
getPath.TransformReport: Gets the path of the output data set
getPositions.GenomeInformation: Gets the physical positions for a set of units
getProbeAffinityFile.ProbeLevelModel: Gets the probe affinities for this model
getResiduals.QualityAssessmentModel: Calculates the residuals from a probe-level model
getRootPath.Model: Gets the root path of this model
getSnpNames.AffymetrixCdfFile: Gets the names of the SNP units
getTags.GenericReporter: Gets the tags of the reporter
getTags.Model: Gets the tags of the output data set
getTags.TransformReport: Gets the tags of the output data set
getTimestamp.AffymetrixCelFile: Gets the timestamp in the CEL header
getUnitGroupCellMap.ChipEffectFile: Gets a (unit, group, cell) index map
getUnitIndices.GenomeInformation: Gets unit indices ordered along the chromosome
getUnitIntensities.AffymetrixCelSet: Gets cell signals for a subset of units and a subset of...
getUnitNames.AffymetrixCdfFile: Gets the names of each unit
getUnitNames.AffymetrixPgfFile: Gets the names of each unit
getUnitTypes.AffymetrixCdfFile: Gets the types of a set of units
getWeights.QualityAssessmentModel: Calculates the weights from the robust fit to a probe-level...
getXAM.ChipEffectFile: Gets the physical position, log-intensities and log-ratios of...
getXAM.ChipEffectSet: Gets the physical position, log-intensities and log-ratios of...
groupUnitsByDimension.AffymetrixCdfFile: Groups units by dimensions
HetLogAddCnPlm: The HetLogAddCnPlm class
HetLogAddPlm: The HetLogAddPlm class
HetLogAddSnpPlm: The HetLogAddSnpPlm class
image270.AffymetrixCelFile: Displays all or a subset of the data spatially
importFromApt.CnChipEffectSet: Imports copy-number estimates from an APT summary file
importFromDChip.AffymetrixCelSet: Imports dChip-exported CEL files
importFromDChip.CnChipEffectSet: Imports copy-number estimates from a dChip result file
isDuplicated.AffymetrixCelSet: Identifies duplicated CEL files
isDuplicated.CnagCfhSet: Identifies duplicated CFH files
isPm.AffymetrixCdfFile: Checks which cells (probes) are PMs and not
isResequenceChip.AffymetrixCdfFile: Static method to check if a CDF is for a resequencing...
isSnpChip.AffymetrixCdfFile: Static method to check if a chip is a mapping (SNP) chip
justRMA: Robust Multichip Analysis (RMA) reproducing the affy package
LimmaBackgroundCorrection: The LimmaBackgroundCorrection class
LinearModelProbeSequenceNormalization: The LinearModelProbeSequenceNormalization class
MatNormalization: The MatNormalization class
MatSmoothing: The MatSmoothing class
MbeiCnPlm: The MbeiCnPlm class
MbeiPlm: The MbeiPlm class
MbeiSnpPlm: The MbeiSnpPlm class
Model: The Model class
MultiArrayUnitModel: The MultiArrayUnitModel class
nbrOfArrays.AffymetrixCelSet: Gets the number of arrays in the file set
nbrOfGroupsPerUnit.AffymetrixCdfFile: Gets the number of groups in each unit
nbrOfSnps.AffymetrixCdfFile: Gets the number of SNPs
Non-documented_objects: Non-documented objects
normalizeQuantile.AffymetrixCelFile: Normalizes the probe intensities to a target empirical...
normalizeQuantile.AffymetrixCelSet: Normalizes samples to have the same empirical distribution
NormExpBackgroundCorrection: The NormExpBackgroundCorrection class
OpticalBackgroundCorrection: The OpticalBackgroundCorrection class
ParameterCelFile: The ParameterCelFile class
ParameterCelSet: The ParameterCelSet class
pdInfo2Cdf: Generates an Affymetrix CDF file from a Platform Design (PD)...
plotBoxplotStats.list: Plots a (merged or non-merged) list of boxplot.stats()...
plotDensity.AffymetrixCelFile: Plots the density of the probe signals on the array
plotDensity.AffymetrixCelSet: Plots the densities of all samples
plotDensity.GenomeInformation: Plots the density of SNPs for a given chromosome
plotImage.AffymetrixCelFile: Displays a spatial plot of a CEL file
plotMvsA.AffymetrixCelFile: Plots log-ratio versus log-intensity in a scatter plot
plotMvsX.AffymetrixCelFile: Plots log-ratio versus another variable in a scatter plot
ProbeAffinityFile: The ProbeAffinityFile class
ProbeLevelModel: The ProbeLevelModel class
ProbeLevelTransform: The ProbeLevelTransform class
ProbeLevelTransform3: The ProbeLevelTransform3 class
process.AbstractProbeSequenceNormalization: Normalizes the data set
process.AdditiveCovariatesNormalization: Normalizes the data set
process.AllelicCrosstalkCalibration: Calibrates the data set
process.ArrayExplorer: Generates image files, scripts and dynamic pages for the...
process.BackgroundCorrection: Processes the data set
process.ChipEffectGroupMerge: Normalizes the data set
process.DChipQuantileNormalization: Normalizes the data set
process.FragmentEquivalentClassNormalization: Normalizes the data set
process.FragmentLengthNormalization: Normalizes the data set
process.GcContentNormalization: Normalizes the data set
process.GcRmaBackgroundCorrection: Performs background correction
process.GenericReporter: Generates report
process.LimmaBackgroundCorrection: Performs background correction
process.MatNormalization: Normalizes the data set
process.MatSmoothing: Processes the data set
process.OpticalBackgroundCorrection: Performs background correction
process.QuantileNormalization: Normalizes the data set
process.ReseqCrosstalkCalibration: Calibrates the data set
process.RmaBackgroundCorrection: Performs background correction
process.ScaleNormalization: Normalizes the data set
process.ScaleNormalization3: Normalizes the data set
process.SpatialReporter: Generates image files, scripts and dynamic pages for the...
process.UnitTypeScaleNormalization: Normalizes the data set
QualityAssessmentFile: The QualityAssessmentFile class
QualityAssessmentModel: The QualityAssessmentModel class
QualityAssessmentSet: The QualityAssessmentSet class
QuantileNormalization: The QuantileNormalization class
randomSeed: Sets and resets the .Random.seed in the global environment
readRawData.AffymetrixCelFile: Gets all or a subset of the fields in a CEL file
readUnits.AffymetrixCdfFile: Reads CDF data unit by unit
readUnits.AffymetrixCelFile: Reads CEL data unit by unit
readUnitsByQuartets.AffymetrixCdfFile: Gets the cell quartets for each base position
readUnits.CnagCfhFile: Reads CEL data unit by unit
readUnits.MultiArrayUnitModel: Reads data unit by unit
readUnits.SingleArrayUnitModel: Reads data unit by unit
ReseqCrosstalkCalibration: The ReseqCrosstalkCalibration class
ResidualFile: The ResidualFile class
ResidualSet: The ResidualSet class
RmaBackgroundCorrection: The RmaBackgroundCorrection class
RmaCnPlm: The RmaCnPlm class
RmaPlm: The RmaPlm class
RmaSnpPlm: The RmaSnpPlm class
ScaleNormalization: The ScaleNormalization class
ScaleNormalization3: The ScaleNormalization3 class
setAlias.GenericReporter: Sets the alias of the report
setAlias.Model: Sets the name alias for the model
setArrays.ArrayExplorer: Sets the arrays
setCdf.AffymetrixCelFile: Sets the CDF structure for this CEL file
setCdf.AffymetrixCelSet: Sets the CDF structure for this CEL set
setCdf.CnagCfhFile: Sets the CDF structure for this CEL file
setCdf.CnagCfhSet: Sets the CDF structure for this CFH set
setRestructor.AffymetrixCdfFile: Specifies a function through which
setTags.Model: Sets the tags to be appended
setupExampleData: Setups example data in the current directory
setupExampleData.AromaAffymetrix: Setups example data in the current directory
SingleArrayUnitModel: The SingleArrayUnitModel class
SmoothMultiarrayModel: The SmoothMultiarrayModel class
SmoothRmaModel: The SmoothRmaModel class
smoothScatterMvsA.AffymetrixCelFile: Plots log-ratio versus log-intensity in a smooth scatter plot
SnpChipEffectFile: The SnpChipEffectFile class
SnpChipEffectGroupMerge: The SnpChipEffectGroupMerge class
SnpChipEffectSet: The SnpChipEffectSet class
SnpInformation: The SnpInformation class
SnpPlm: The SnpPlm interface class
SnpProbeAffinityFile: The SnpProbeAffinityFile class
SpatialReporter: The SpatialReporter class
TransformReport: The TransformReport class
UgpGenomeInformation: The UgpGenomeInformation class
UnitModel: The UnitModel class
UnitTypeScaleNormalization: The UnitTypeScaleNormalization class
updateUnits.AffymetrixCelFile: Updates CEL data unit by unit
verify.GenomeInformation: Verifies the correctness of the underlying file
verify.SnpInformation: Verifies the correctness of the underlying file
WeightsFile: The WeightsFile class
WeightsSet: The WeightsSet class
writeCdf.AffyGenePDInfo: Generates an Affymetrix CDF file from a Platform Design (PD)...
writeImage.AffymetrixCelFile: Writes a spatial image of the signals in the CEL file

Functions

ASCRMAv2 Man page
AbstractProbeSequenceNormalization Man page
AbstractProbeSequenceNormalization.process Man page
AdditiveCovariatesNormalization Man page
AdditiveCovariatesNormalization.process Man page
AffineCnPlm Man page
AffinePlm Man page
AffinePlm.getFitUnitGroupFunction Man page
AffineSnpPlm Man page
AffyGenePDInfo.writeCdf Man page
AffymetrixAptSummaryFile Man page
AffymetrixCdfFile Man page
AffymetrixCdfFile$findByChipType Man page
AffymetrixCdfFile$fromFile Man page
AffymetrixCdfFile.compare Man page
AffymetrixCdfFile.computeAffinities Man page
AffymetrixCdfFile.convert Man page
AffymetrixCdfFile.convertUnits Man page
AffymetrixCdfFile.createExonByTranscriptCdf Man page
AffymetrixCdfFile.createMonoCell Man page
AffymetrixCdfFile.createMonocellCdf Man page
AffymetrixCdfFile.createUnique Man page
AffymetrixCdfFile.createUniqueCdf Man page
AffymetrixCdfFile.findByChipType Man page
AffymetrixCdfFile.fromFile Man page
AffymetrixCdfFile.getAlleleCellPairs Man page
AffymetrixCdfFile.getAlleleProbePairs Man page
AffymetrixCdfFile.getAlleleProbePairs3 Man page
AffymetrixCdfFile.getCellIndices Man page
AffymetrixCdfFile.getCnNames Man page
AffymetrixCdfFile.getGenomeInformation Man page
AffymetrixCdfFile.getHeader Man page
AffymetrixCdfFile.getSnpNames Man page
AffymetrixCdfFile.getUnitNames Man page
AffymetrixCdfFile.getUnitTypes Man page
AffymetrixCdfFile.groupUnitsByDimension Man page
AffymetrixCdfFile.isPm Man page
AffymetrixCdfFile.isResequenceChip Man page
AffymetrixCdfFile.isSnpChip Man page
AffymetrixCdfFile.nbrOfGroupsPerUnit Man page
AffymetrixCdfFile.nbrOfSnps Man page
AffymetrixCdfFile.readUnits Man page
AffymetrixCdfFile.readUnitsByQuartets Man page
AffymetrixCdfFile.setRestructor Man page
AffymetrixCelFile Man page
AffymetrixCelFile$allocateFromCdf Man page
AffymetrixCelFile$clearData Man page
AffymetrixCelFile$fromFile Man page
AffymetrixCelFile.allocateFromCdf Man page
AffymetrixCelFile.clearData Man page
AffymetrixCelFile.createFrom Man page
AffymetrixCelFile.fitQuantileNormFcn Man page
AffymetrixCelFile.fromFile Man page
AffymetrixCelFile.getCdf Man page
AffymetrixCelFile.getChipType Man page
AffymetrixCelFile.getData Man page
AffymetrixCelFile.getHeader Man page
AffymetrixCelFile.getImage Man page
AffymetrixCelFile.getTimestamp Man page
AffymetrixCelFile.image270 Man page
AffymetrixCelFile.normalizeQuantile Man page
AffymetrixCelFile.plotDensity Man page
AffymetrixCelFile.plotImage Man page
AffymetrixCelFile.plotMvsA Man page
AffymetrixCelFile.plotMvsX Man page
AffymetrixCelFile.readRawData Man page
AffymetrixCelFile.readUnits Man page
AffymetrixCelFile.setCdf Man page
AffymetrixCelFile.smoothScatterMvsA Man page
AffymetrixCelFile.updateUnits Man page
AffymetrixCelFile.writeImage Man page
AffymetrixCelSet Man page
AffymetrixCelSet$importFromDChip Man page
AffymetrixCelSet.as.AffymetrixCelSet Man page
AffymetrixCelSet.as.character Man page
AffymetrixCelSet.averageQuantile Man page
AffymetrixCelSet.calculateParametersGsb Man page
AffymetrixCelSet.extractAffyBatch Man page
AffymetrixCelSet.extractFeatureSet Man page
AffymetrixCelSet.extractMatrix Man page
AffymetrixCelSet.extractSnpFeatureSet Man page
AffymetrixCelSet.getAverageFile Man page
AffymetrixCelSet.getCdf Man page
AffymetrixCelSet.getChipType Man page
AffymetrixCelSet.getIntensities Man page
AffymetrixCelSet.getUnitIntensities Man page
AffymetrixCelSet.importFromDChip Man page
AffymetrixCelSet.isDuplicated Man page
AffymetrixCelSet.nbrOfArrays Man page
AffymetrixCelSet.normalizeQuantile Man page
AffymetrixCelSet.plotDensity Man page
AffymetrixCelSet.setCdf Man page
AffymetrixCelSetReporter Man page
AffymetrixCelSetReporter.getDataSet Man page
AffymetrixCelSetTuple Man page
AffymetrixCnChpFile Man page
AffymetrixCnChpSet Man page
AffymetrixCnChpSet.as.AffymetrixCnChpSet Man page
AffymetrixCnChpSet.as.character Man page
AffymetrixCsvFile Man page
AffymetrixCsvGenomeInformation Man page
AffymetrixFile Man page
AffymetrixFileSet Man page
AffymetrixFileSet$byPath Man page
AffymetrixFileSet.as.AffymetrixFileSet Man page
AffymetrixFileSet.byPath Man page
AffymetrixFileSetReporter Man page
AffymetrixNetAffxCsvFile Man page
AffymetrixPgfFile Man page
AffymetrixPgfFile$findByChipType Man page
AffymetrixPgfFile$fromFile Man page
AffymetrixPgfFile.findByChipType Man page
AffymetrixPgfFile.fromFile Man page
AffymetrixPgfFile.getHeader Man page
AffymetrixPgfFile.getUnitNames Man page
AffymetrixPlatform Man page
AffymetrixProbeTabFile Man page
AffymetrixTabularFile Man page
AffymetrixTsvFile Man page
AlleleSummation Man page
AlleleSummation.getChipEffectSet Man page
AllelicCrosstalkCalibration Man page
AllelicCrosstalkCalibration.process Man page
AromaAffymetrix Man page
AromaAffymetrix.setupExampleData Man page
AromaCellMatchScoreFile Man page
AromaChipTypeAnnotationFile Man page
AromaChipTypeAnnotationFile$byChipType Man page
AromaChipTypeAnnotationFile$fromFile Man page
AromaChipTypeAnnotationFile.byChipType Man page
AromaChipTypeAnnotationFile.byName Man page
AromaChipTypeAnnotationFile.findByChipType Man page
AromaChipTypeAnnotationFile.fromFile Man page
AromaChipTypeAnnotationFile.getHeader Man page
AromaPipeline Man page
AromaUfcFile Man page
AromaUnitTabularBinaryFile$allocateFromCdf Man page
AromaUnitTabularBinaryFile.allocateFromCdf Man page
ArrayExplorer Man page
ArrayExplorer.getDataSet Man page
ArrayExplorer.process Man page
ArrayExplorer.setArrays Man page
AvgCnPlm Man page
AvgPlm Man page
AvgPlm.getFitUnitGroupFunction Man page
AvgSnpPlm Man page
BackgroundCorrection Man page
BackgroundCorrection.process Man page
BaseCountNormalization Man page
BasePositionNormalization Man page
ChipEffectFile Man page
ChipEffectFile$fromDataFile Man page
ChipEffectFile.fromDataFile Man page
ChipEffectFile.getAM Man page
ChipEffectFile.getCellIndices Man page
ChipEffectFile.getCellMap Man page
ChipEffectFile.getUnitGroupCellMap Man page
ChipEffectFile.getXAM Man page
ChipEffectGroupMerge Man page
ChipEffectGroupMerge.process Man page
ChipEffectSet Man page
ChipEffectSet.calculateBaseline Man page
ChipEffectSet.extractExpressionSet Man page
ChipEffectSet.getAM Man page
ChipEffectSet.getBaseline Man page
ChipEffectSet.getXAM Man page
ChipEffectSetTuple Man page
ChipEffectTransform Man page
CnChipEffectFile Man page
CnChipEffectFile.getCellIndices Man page
CnChipEffectSet Man page
CnChipEffectSet$importFromApt Man page
CnChipEffectSet$importFromDChip Man page
CnChipEffectSet.importFromApt Man page
CnChipEffectSet.importFromDChip Man page
CnChipEffectSetTuple Man page
CnPlm Man page
CnProbeAffinityFile Man page
CnProbeAffinityFile.getCellIndices Man page
CnagCfhFile Man page
CnagCfhFile$fromFile Man page
CnagCfhFile.fromFile Man page
CnagCfhFile.getCdf Man page
CnagCfhFile.getChipType Man page
CnagCfhFile.getHeader Man page
CnagCfhFile.readUnits Man page
CnagCfhFile.setCdf Man page
CnagCfhSet Man page
CnagCfhSet.as.CnagCfhSet Man page
CnagCfhSet.as.character Man page
CnagCfhSet.getAverageFile Man page
CnagCfhSet.getCdf Man page
CnagCfhSet.isDuplicated Man page
CnagCfhSet.setCdf Man page
CrlmmModel Man page
CrlmmParametersFile Man page
CrlmmParametersSet Man page
DChipCdfBinFile Man page
DChipDcpFile Man page
DChipDcpSet Man page
DChipDcpSet.as.DChipDcpSet Man page
DChipDcpSet.as.character Man page
DChipGenomeInformation Man page
DChipGenomeInformation.byChipType Man page
DChipQuantileNormalization Man page
DChipQuantileNormalization.process Man page
DChipSnpInformation Man page
DChipSnpInformation.byChipType Man page
Env2Cdf Man page
ExonChipEffectFile Man page
ExonChipEffectFile.getCellIndices Man page
ExonChipEffectSet Man page
ExonProbeAffinityFile Man page
ExonProbeAffinityFile.getCellIndices Man page
ExonRmaPlm Man page
ExonRmaPlm.getFitUnitGroupFunction Man page
FirmaFile Man page
FirmaFile.getCellIndices Man page
FirmaModel Man page
FirmaModel.calculateResidualSet Man page
FirmaModel.calculateResiduals Man page
FirmaModel.findUnitsTodo Man page
FirmaModel.fit Man page
FirmaModel.getFirmaScores Man page
FirmaModel.getFirmaSet Man page
FirmaModel.getFitUnitGroupFunction Man page
FirmaSet Man page
FragmentEquivalentClassNormalization Man page
FragmentEquivalentClassNormalization.process Man page
FragmentLengthNormalization Man page
FragmentLengthNormalization.process Man page
GcContentNormalization Man page
GcContentNormalization.process Man page
GcContentNormalization2 Man page
GcRmaBackgroundCorrection Man page
GcRmaBackgroundCorrection.process Man page
GenericReporter Man page
GenericReporter.getAlias Man page
GenericReporter.getName Man page
GenericReporter.getTags Man page
GenericReporter.process Man page
GenericReporter.setAlias Man page
GenomeInformation Man page
GenomeInformation$byChipType Man page
GenomeInformation$fromCdf Man page
GenomeInformation.byChipType Man page
GenomeInformation.fromCdf Man page
GenomeInformation.getChipType Man page
GenomeInformation.getData Man page
GenomeInformation.getPositions Man page
GenomeInformation.getUnitIndices Man page
GenomeInformation.plotDensity Man page
GenomeInformation.verify Man page
HetLogAddCnPlm Man page
HetLogAddPlm Man page
HetLogAddPlm.getFitUnitGroupFunction Man page
HetLogAddSnpPlm Man page
LimmaBackgroundCorrection Man page
LimmaBackgroundCorrection.process Man page
LinearModelProbeSequenceNormalization Man page
MatNormalization Man page
MatNormalization.process Man page
MatSmoothing Man page
MatSmoothing.process Man page
MbeiCnPlm Man page
MbeiPlm Man page
MbeiPlm.getFitUnitGroupFunction Man page
MbeiSnpPlm Man page
Model Man page
Model.fit Man page
Model.getAlias Man page
Model.getCdf Man page
Model.getDataSet Man page
Model.getFullName Man page
Model.getName Man page
Model.getPath Man page
Model.getRootPath Man page
Model.getTags Man page
Model.setAlias Man page
Model.setTags Man page
MultiArrayUnitModel Man page
MultiArrayUnitModel$getFitUnitGroupFunction Man page
MultiArrayUnitModel.getFitUnitGroupFunction Man page
MultiArrayUnitModel.readUnits Man page
Non-documented objects Man page
NormExpBackgroundCorrection Man page
OpticalBackgroundCorrection Man page
OpticalBackgroundCorrection.process Man page
ParameterCelFile Man page
ParameterCelSet Man page
ParameterCelSet.extractDataFrame Man page
ParameterCelSet.extractMatrix Man page
ProbeAffinityFile Man page
ProbeAffinityFile.getCellIndices Man page
ProbeLevelModel Man page
ProbeLevelModel.findUnitsTodo Man page
ProbeLevelModel.fit Man page
ProbeLevelModel.getChipEffectSet Man page
ProbeLevelModel.getChipEffects Man page
ProbeLevelModel.getProbeAffinities Man page
ProbeLevelModel.getProbeAffinityFile Man page
ProbeLevelTransform Man page
ProbeLevelTransform3 Man page
QualityAssessmentFile Man page
QualityAssessmentModel Man page
QualityAssessmentModel.getResiduals Man page
QualityAssessmentModel.getWeights Man page
QualityAssessmentSet Man page
QuantileNormalization Man page
QuantileNormalization.process Man page
ReseqCrosstalkCalibration Man page
ReseqCrosstalkCalibration.process Man page
ResidualFile Man page
ResidualFile.getCellIndices Man page
ResidualSet Man page
RmaBackgroundCorrection Man page
RmaBackgroundCorrection.process Man page
RmaCnPlm Man page
RmaPlm Man page
RmaPlm.getFitUnitGroupFunction Man page
RmaSnpPlm Man page
ScaleNormalization Man page
ScaleNormalization.process Man page
ScaleNormalization3 Man page
ScaleNormalization3.process Man page
SingleArrayUnitModel Man page
SingleArrayUnitModel$getFitUnitGroupFunction Man page
SingleArrayUnitModel.fit Man page
SingleArrayUnitModel.getFitUnitGroupFunction Man page
SingleArrayUnitModel.readUnits Man page
SmoothMultiarrayModel Man page
SmoothMultiarrayModel.fit Man page
SmoothRmaModel Man page
SmoothSaModel Man page
SnpChipEffectFile Man page
SnpChipEffectFile.getCellIndices Man page
SnpChipEffectGroupMerge Man page
SnpChipEffectSet Man page
SnpInformation Man page
SnpInformation$fromCdf Man page
SnpInformation.byChipType Man page
SnpInformation.fromCdf Man page
SnpInformation.getChipType Man page
SnpInformation.getData Man page
SnpInformation.verify Man page
SnpPlm Man page
SnpProbeAffinityFile Man page
SnpProbeAffinityFile.getCellIndices Man page
SpatialReporter Man page
SpatialReporter.process Man page
SpatialRowColumnNormalization Man page
Transform Man page
Transform.getOutputDataSet Man page
TransformReport Man page
TransformReport.getFullName Man page
TransformReport.getInputDataSet Man page
TransformReport.getName Man page
TransformReport.getOutputDataSet Man page
TransformReport.getPath Man page
TransformReport.getTags Man page
UflSnpInformation Man page
UgpGenomeInformation Man page
UgpGenomeInformation$byChipType Man page
UgpGenomeInformation.byChipType Man page
UnitModel Man page
UnitModel.findUnitsTodo Man page
UnitModel.getCellIndices Man page
UnitTypeScaleNormalization Man page
UnitTypeScaleNormalization.process Man page
WeightsFile Man page
WeightsFile.getCellIndices Man page
WeightsSet Man page
addColorMap Man page
addColorMap.ArrayExplorer Man page
addColorMap.SpatialReporter Man page
addExclCells Man page
addExclCells.DChipQuantileNormalization Man page
allocate.AromaCellMatchScoreFile Man page
allocate.CrlmmParametersFile Man page
allocateFromCdf Man page
allocateFromCdf,AffymetrixCelFile-method Man page
allocateFromCdf,AromaUnitTabularBinaryFile-method Man page
allocateFromCdf.AffymetrixCelFile Man page
allocateFromCdf.AromaCellCpgFile Man page
allocateFromCdf.AromaCellMatchScoreFile Man page
allocateFromCdf.AromaCellPositionFile Man page
allocateFromCdf.AromaCellSequenceFile Man page
allocateFromCdf.AromaUfcFile Man page
allocateFromCdf.AromaUflFile Man page
allocateFromCdf.AromaUnitGcContentFile Man page
allocateFromCdf.AromaUnitTabularBinaryFile Man page
annotateMvsA Man page
annotateMvsA.AffymetrixCelFile Man page
annotation Source code
append.AffymetrixCelSet Man page
append.CnagCfhSet Man page
applyAnyOrder Man page
applyAnyOrder.CopyNumberChromosomalModel Man page
applyCCF0 Man page
applyCCF0.CopyNumberChromosomalModel Man page
applyCFC0 Man page
applyCFC0.CopyNumberChromosomalModel Man page
applyCdfGroups Source code
applyToUnitIntensities Man page
applyToUnitIntensities.AffymetrixCelSet Man page
aroma.affymetrix Man page
aroma.affymetrix-package Man page
as.AffymetrixCelSet Man page
as.AffymetrixCelSet,AffymetrixCelSet-method Man page
as.AffymetrixCelSet.AffymetrixCelSet Man page
as.AffymetrixCelSet.default Man page
as.AffymetrixCelSet.list Man page
as.AffymetrixCnChpSet Man page
as.AffymetrixCnChpSet,AffymetrixCnChpSet-method Man page
as.AffymetrixCnChpSet.AffymetrixCnChpSet Man page
as.AffymetrixCnChpSet.default Man page
as.AffymetrixCnChpSet.list Man page
as.AffymetrixFileSet Man page
as.AffymetrixFileSet,AffymetrixFileSet-method Man page
as.AffymetrixFileSet.AffymetrixFileSet Man page
as.AffymetrixFileSet.default Man page
as.AffymetrixFileSet.list Man page
as.ChipEffectSetTuple Man page
as.ChipEffectSetTuple.ChipEffectSetTuple Man page
as.ChipEffectSetTuple.default Man page
as.CnChipEffectSetTuple Man page
as.CnChipEffectSetTuple.CnChipEffectSetTuple Man page
as.CnChipEffectSetTuple.default Man page
as.CnagCfhSet Man page
as.CnagCfhSet,CnagCfhSet-method Man page
as.CnagCfhSet.CnagCfhSet Man page
as.CnagCfhSet.default Man page
as.CnagCfhSet.list Man page
as.CopyNumberDataSetTuple.CnChipEffectSet Man page
as.DChipDcpSet Man page
as.DChipDcpSet,DChipDcpSet-method Man page
as.DChipDcpSet.DChipDcpSet Man page
as.DChipDcpSet.default Man page
as.DChipDcpSet.list Man page
as.character,AffymetrixCelSet-method Man page
as.character,AffymetrixCnChpSet-method Man page
as.character,CnagCfhSet-method Man page
as.character,DChipDcpSet-method Man page
as.character.AffymetrixCdfFile Man page
as.character.AffymetrixCelFile Man page
as.character.AffymetrixCelSet Man page
as.character.AffymetrixCelSetReporter Man page
as.character.AffymetrixCnChpFile Man page
as.character.AffymetrixCnChpSet Man page
as.character.AffymetrixPgfFile Man page
as.character.AffymetrixProbeTabFile Man page
as.character.AromaChipTypeAnnotationFile Man page
as.character.ArrayExplorer Man page
as.character.ChipEffectFile Man page
as.character.ChipEffectSet Man page
as.character.CnagCfhFile Man page
as.character.CnagCfhSet Man page
as.character.DChipCdfBinFile Man page
as.character.DChipDcpFile Man page
as.character.DChipDcpSet Man page
as.character.DChipQuantileNormalization Man page
as.character.FirmaModel Man page
as.character.GenericReporter Man page
as.character.GenomeInformation Man page
as.character.Model Man page
as.character.ProbeAffinityFile Man page
as.character.QualityAssessmentModel Man page
as.character.ResidualFile Man page
as.character.ResidualSet Man page
as.character.SmoothMultiarrayModel Man page
as.character.SnpInformation Man page
as.character.SpatialReporter Man page
as.character.TransformReport Man page
as.character.WeightsFile Man page
as.character.WeightsSet Man page
assayData Source code
assertAnnotationData Man page
assertAnnotationData.ASCRMAv2 Man page
averageQuantile Man page
averageQuantile,AffymetrixCelSet-method Man page
averageQuantile.AffymetrixCelSet Man page
bgAdjustGcrma Man page
bgAdjustOptical Man page
bgAdjustRma Man page
boxplotStats Man page
boxplotStats.ChipEffectSet Man page
bpmapCluster2Cdf Man page
bpmapCluster2Cdf.default Man page
byChipType,AromaChipTypeAnnotationFile-method Man page
byChipType,DChipGenomeInformation-method Man page
byChipType,DChipSnpInformation-method Man page
byChipType,GenomeInformation-method Man page
byChipType,SnpInformation-method Man page
byChipType,UgpGenomeInformation-method Man page
byChipType.AffymetrixCsvGenomeInformation Man page
byChipType.AffymetrixProbeTabFile Man page
byChipType.AffymetrixTabularFile Man page
byChipType.AffymetrixTsvFile Man page
byChipType.AromaCellMatchScoreFile Man page
byChipType.AromaChipTypeAnnotationFile Man page
byChipType.DChipCdfBinFile Man page
byChipType.DChipGenomeInformation Man page
byChipType.DChipSnpInformation Man page
byChipType.GenomeInformation Man page
byChipType.SnpInformation Man page
byChipType.UflSnpInformation Man page
byChipType.UgpGenomeInformation Man page
byName,AromaChipTypeAnnotationFile-method Man page
byName.AffymetrixCelSet Man page
byName.AffymetrixCnChpSet Man page
byName.AromaChipTypeAnnotationFile Man page
byName.CnagCfhSet Man page
byName.CrlmmParametersSet Man page
byName.DChipDcpSet Man page
byPath,AffymetrixFileSet-method Man page
byPath.AffymetrixCelSet Man page
byPath.AffymetrixCelSetTuple Man page
byPath.AffymetrixCnChpSet Man page
byPath.AffymetrixFileSet Man page
byPath.ChipEffectSet Man page
byPath.CnChipEffectSet Man page
byPath.CnagCfhSet Man page
byPath.CrlmmParametersSet Man page
byPath.DChipDcpSet Man page
byPath.ExonChipEffectSet Man page
byPath.FirmaSet Man page
byPath.ResidualSet Man page
byPath.SnpChipEffectSet Man page
byPath.WeightsSet Man page
calcRawCnStats Man page
calcRawCnStats.CopyNumberChromosomalModel Man page
calcRawCnStats.default Man page
calculateAffinities Man page
calculateAffinities.GcRmaBackgroundCorrection Man page
calculateAverages Man page
calculateAverages.FragmentEquivalentClassNormalization Man page
calculateBaseline Man page
calculateBaseline,ChipEffectSet-method Man page
calculateBaseline.ChipEffectSet Man page
calculateConfidenceScores Man page
calculateConfidenceScores.CrlmmModel Man page
calculateFieldBoxplotStats Man page
calculateFieldBoxplotStats.ChipEffectSet Man page
calculateMargins Man page
calculateMargins.SpatialReporter Man page
calculateNuseBoxplotStats Man page
calculateNuseBoxplotStats.ChipEffectSet Man page
calculateParametersGsb Man page
calculateParametersGsb,AffymetrixCelSet-method Man page
calculateParametersGsb.AffymetrixCelSet Man page
calculateResidualSet Man page
calculateResidualSet,FirmaModel-method Man page
calculateResidualSet.FirmaModel Man page
calculateResidualSet.ProbeLevelModel Man page
calculateResiduals,FirmaModel-method Man page
calculateResiduals.FirmaModel Man page
calculateRleBoxplotStats Man page
calculateRleBoxplotStats.ChipEffectSet Man page
calculateTargetDistribution Man page
calculateTargetDistribution.QuantileNormalization Man page
calculateWeights Man page
calculateWeights.ExonRmaPlm Man page
calculateWeights.FirmaModel Man page
calculateWeights.ProbeLevelModel Man page
calibrateMultiscan Source code
calibrateOne Man page
calibrateOne.ReseqCrosstalkCalibration Man page
cdfAddPlasqTypes Source code
cdfHeaderToCelHeader Source code
cdfMergeGroups Man page Source code
cleanPlatformName Source code
clearCache.AffymetrixCelSet Man page
clearData Man page
clearData,AffymetrixCelFile-method Man page
clearData.AffymetrixCelFile Man page
clone.AffymetrixCelFile Man page
clone.AffymetrixCelSet Man page
clone.AffymetrixCnChpFile Man page
clone.CnagCfhFile Man page
clone.CnagCfhSet Man page
compare Man page
compare,AffymetrixCdfFile-method Man page
compare.AffymetrixCdfFile Man page
compareCdfs Source code
computeAffinities Man page
computeAffinities,AffymetrixCdfFile-method Man page
computeAffinities.AffymetrixCdfFile Man page
computeAffinitiesByACS Man page
computeAffinitiesByACS.AffymetrixCdfFile Man page
convert Man page
convert,AffymetrixCdfFile-method Man page
convert.AffymetrixCdfFile Man page
convertCdf Source code
convertCel Source code
convertToUnique Man page
convertToUnique.AffymetrixCelSet Man page
convertUnits Man page
convertUnits,AffymetrixCdfFile-method Man page
convertUnits.AffymetrixCdfFile Man page
createCel Source code
createExonByTranscriptCdf Man page
createExonByTranscriptCdf,AffymetrixCdfFile-method Man page
createExonByTranscriptCdf.AffymetrixCdfFile Man page
createFrom Man page
createFrom,AffymetrixCelFile-method Man page
createFrom.AffymetrixCelFile Man page
createMonoCell,AffymetrixCdfFile-method Man page
createMonoCell.AffymetrixCdfFile Man page
createMonocellCdf Man page
createMonocellCdf,AffymetrixCdfFile-method Man page
createMonocellCdf.AffymetrixCdfFile Man page
createOutputTuple Man page
createOutputTuple.SmoothMultiarrayModel Man page
createParamCdf Man page
createParamCdf.ChipEffectFile Man page
createParamCdf.FirmaFile Man page
createUnique,AffymetrixCdfFile-method Man page
createUnique.AffymetrixCdfFile Man page
createUniqueCdf Man page
createUniqueCdf,AffymetrixCdfFile-method Man page
createUniqueCdf.AffymetrixCdfFile Man page
decode Man page
decode.ParameterCelFile Man page
dim.DChipDcpFile Man page
doASCRMAv1 Man page
doASCRMAv1.default Man page
doASCRMAv2 Man page
doASCRMAv2.default Man page
doCRMAv1 Man page
doCRMAv1.AffymetrixCelSet Man page
doCRMAv1.default Man page
doCRMAv2 Man page
doCRMAv2.AffymetrixCelSet Man page
doCRMAv2.default Man page
doFIRMA Man page
doFIRMA.AffymetrixCelSet Man page
doFIRMA.default Man page
doGCRMA Man page
doGCRMA.AffymetrixCelSet Man page
doGCRMA.default Man page
doRMA Man page
doRMA.AffymetrixCelSet Man page
doRMA.default Man page
dropCellsFromCdfList Man page Source code
encode Man page
encode.ParameterCelFile Man page
env2Cdf Man page Source code
excludeChrXFromFit Man page
excludeChrXFromFit.DChipQuantileNormalization Man page
exportAromaSignalBinaryFileList Man page
exportAromaSignalBinaryFileList.CnChipEffectFile Man page
exportTotalAndFracB Man page
exportTotalAndFracB.CnChipEffectFile Man page
exportTotalAndFracB.CnChipEffectSet Man page
exportTotalAndFracB.DChipDcpSet Man page
exportTotalAndFracB.SnpChipEffectFile Man page
exportTotalAndFracB.SnpChipEffectSet Man page
exportTotalCnRatioSet.AffymetrixCnChpSet Man page
extractAffyBatch Man page
extractAffyBatch,AffymetrixCelSet-method Man page
extractAffyBatch.AffymetrixCelSet Man page
extractAffyBatch.ChipEffectSet Man page
extractAlleleSet Man page
extractAlleleSet.SnpChipEffectSet Man page
extractCNT Man page
extractCNT.SnpChipEffectFile Man page
extractCNT.SnpChipEffectSet Man page
extractChromosomalDataFrame Man page
extractChromosomalDataFrame.ChipEffectFile Man page
extractChromosomalDataFrame.ChipEffectSet Man page
extractDataFrame Man page
extractDataFrame,ParameterCelSet-method Man page
extractDataFrame.ParameterCelFile Man page
extractDataFrame.ParameterCelSet Man page
extractExpressionSet Man page
extractExpressionSet,ChipEffectSet-method Man page
extractExpressionSet.ChipEffectSet Man page
extractFeatureSet Man page
extractFeatureSet,AffymetrixCelSet-method Man page
extractFeatureSet.AffymetrixCelSet Man page
extractLogRatios Man page
extractLogRatios.AffymetrixCnChpFile Man page
extractLogRatios.AffymetrixCnChpSet Man page
extractMatrix,AffymetrixCelSet-method Man page
extractMatrix,ParameterCelSet-method Man page
extractMatrix.AffymetrixCelFile Man page
extractMatrix.AffymetrixCelSet Man page
extractMatrix.ChipEffectFile Man page
extractMatrix.ChipEffectSet Man page
extractMatrix.FirmaFile Man page
extractMatrix.FirmaSet Man page
extractMatrix.ParameterCelFile Man page
extractMatrix.ParameterCelSet Man page
extractSnpCnvQSet Man page
extractSnpCnvQSet.SnpChipEffectSet Man page
extractSnpFeatureSet Man page
extractSnpFeatureSet,AffymetrixCelSet-method Man page
extractSnpFeatureSet.AffymetrixCelSet Man page
extractSnpQSet Man page
extractSnpQSet.SnpChipEffectSet Man page
extractTheta Man page
extractTheta.ChipEffectFile Man page
extractTheta.ChipEffectSet Man page
extractTheta.CnChipEffectFile Man page
extractTheta.CnChipEffectSet Man page
extractTheta.DChipDcpFile Man page
extractTheta.DChipDcpSet Man page
extractTheta.SnpChipEffectFile Man page
extractTheta.SnpChipEffectSet Man page
extractTheta.SnpCnvQSet Man page
extractTheta.SnpQSet Man page
extractTotalAndFracB Man page
extractTotalAndFracB.SnpChipEffectFile Man page
extractTotalAndFreqB Man page
extractTotalAndFreqB.CnChipEffectFile Man page
extractTotalAndFreqB.CnChipEffectSet Man page
extractTotalAndFreqB.SnpChipEffectSet Man page
extractTotalAndFreqB.default Man page
featureNames Source code
findByCdf2 Man page
findByCdf2.default Man page
findByChipType,AffymetrixCdfFile-method Man page
findByChipType,AffymetrixPgfFile-method Man page
findByChipType,AromaChipTypeAnnotationFile-method Man page
findByChipType.AffymetrixCdfFile Man page
findByChipType.AffymetrixCsvFile Man page
findByChipType.AffymetrixCsvGenomeInformation Man page
findByChipType.AffymetrixNetAffxCsvFile Man page
findByChipType.AffymetrixPgfFile Man page
findByChipType.AffymetrixProbeTabFile Man page
findByChipType.AffymetrixTabularFile Man page
findByChipType.AffymetrixTsvFile Man page
findByChipType.AromaChipTypeAnnotationFile Man page
findByChipType.DChipCdfBinFile Man page
findByChipType.DChipGenomeInformation Man page
findByChipType.DChipSnpInformation Man page
findByChipType.UflSnpInformation Man page
findByChipType.UgpGenomeInformation Man page
findByName.AffymetrixCelSet Man page
findByName.AffymetrixCnChpSet Man page
findByName.ChipEffectSet Man page
findByName.CnagCfhSet Man page
findByName.DChipDcpSet Man page
findCdf Source code
findTargetDistributionFile Man page
findTargetDistributionFile.QuantileNormalization Man page
findUnitsTodo,FirmaModel-method Man page
findUnitsTodo,ProbeLevelModel-method Man page
findUnitsTodo,UnitModel-method Man page
findUnitsTodo.AlleleSummation Man page
findUnitsTodo.ChipEffectFile Man page
findUnitsTodo.ChipEffectSet Man page
findUnitsTodo.CrlmmModel Man page
findUnitsTodo.CrlmmParametersFile Man page
findUnitsTodo.CrlmmParametersSet Man page
findUnitsTodo.ExonChipEffectSet Man page
findUnitsTodo.FirmaFile Man page
findUnitsTodo.FirmaModel Man page
findUnitsTodo.FirmaSet Man page
findUnitsTodo.ProbeLevelModel Man page
findUnitsTodo.QualityAssessmentFile Man page
findUnitsTodo.ResidualFile Man page
findUnitsTodo.ResidualSet Man page
findUnitsTodo.UnitModel Man page
findUnitsTodo.WeightsFile Man page
findUnitsTodo.WeightsSet Man page
fit,FirmaModel-method Man page
fit,Model-method Man page
fit,ProbeLevelModel-method Man page
fit,SingleArrayUnitModel-method Man page
fit,SmoothMultiarrayModel-method Man page
fit.CrlmmModel Man page
fit.FirmaModel Man page
fit.Model Man page
fit.ProbeLevelModel Man page
fit.SingleArrayUnitModel Man page
fit.SmoothMultiarrayModel Man page
fitCnProbes Man page
fitCnProbes.UnitModel Man page
fitOne Man page
fitOne.AbstractProbeSequenceNormalization Man page
fitOne.BaseCountNormalization Man page
fitOne.LinearModelProbeSequenceNormalization Man page
fitOne.MatNormalization Man page
fitOne.ReseqCrosstalkCalibration Man page
fitOne.ScaleNormalization3 Man page
fitOne.UnitTypeScaleNormalization Man page
fitOneArray Man page
fitOneArray.SingleArrayUnitModel Man page
fitOneChromosome Man page
fitOneChromosome.SmoothMultiarrayModel Man page
fitPlasqUnit Man page
fitPlasqUnit.matrix Man page
fitQuantileNormFcn Man page
fitQuantileNormFcn,AffymetrixCelFile-method Man page
fitQuantileNormFcn.AffymetrixCelFile Man page
fixSearchPath.AromaAffymetrix Man page
fromCdf Man page
fromCdf,GenomeInformation-method Man page
fromCdf,SnpInformation-method Man page
fromCdf.AffymetrixProbeTabFile Man page
fromCdf.GenomeInformation Man page
fromCdf.SnpInformation Man page
fromDataFile Man page
fromDataFile,ChipEffectFile-method Man page
fromDataFile.ChipEffectFile Man page
fromDataFile.FirmaFile Man page
fromDataFile.ResidualFile Man page
fromDataFile.WeightsFile Man page
fromDataSet Man page
fromDataSet.ChipEffectSet Man page
fromDataSet.FirmaSet Man page
fromDataSet.GenomeInformation Man page
fromDataSet.ResidualSet Man page
fromDataSet.SnpInformation Man page
fromDataSet.WeightsSet Man page
fromFile,AffymetrixCdfFile-method Man page
fromFile,AffymetrixCelFile-method Man page
fromFile,AffymetrixPgfFile-method Man page
fromFile,AromaChipTypeAnnotationFile-method Man page
fromFile,CnagCfhFile-method Man page
fromFile.AffymetrixCdfFile Man page
fromFile.AffymetrixCelFile Man page
fromFile.AffymetrixCnChpFile Man page
fromFile.AffymetrixPgfFile Man page
fromFile.AromaChipTypeAnnotationFile Man page
fromFile.CnagCfhFile Man page
fromFile.DChipCdfBinFile Man page
fromFile.DChipDcpFile Man page
geometry Source code
getACSFile Man page
getACSFile.AffymetrixCdfFile Man page
getAM,ChipEffectFile-method Man page
getAM,ChipEffectSet-method Man page
getAM.ChipEffectFile Man page
getAM.ChipEffectSet Man page
getAlias,GenericReporter-method Man page
getAlias,Model-method Man page
getAlias.ArrayExplorer Man page
getAlias.GenericReporter Man page
getAlias.Model Man page
getAlias.TransformReport Man page
getAlleleCellPairs Man page
getAlleleCellPairs,AffymetrixCdfFile-method Man page
getAlleleCellPairs.AffymetrixCdfFile Man page
getAlleleProbePairs Man page
getAlleleProbePairs,AffymetrixCdfFile-method Man page
getAlleleProbePairs.AffymetrixCdfFile Man page
getAlleleProbePairs2 Man page
getAlleleProbePairs2.AffymetrixCdfFile Man page
getAlleleProbePairs3 Man page
getAlleleProbePairs3,AffymetrixCdfFile-method Man page
getAlleleProbePairs3.AffymetrixCdfFile Man page
getAm Man page
getAm.AffymetrixCelFile Man page
getAromaCellMatchScoreFile Man page
getAromaCellMatchScoreFile.MatNormalization Man page
getAromaCellPositionFile Man page
getAromaCellPositionFile.MatSmoothing Man page
getAromaCellSequenceFile Man page
getAromaCellSequenceFile.AbstractProbeSequenceNormalization Man page
getAromaCellSequenceFile.AffymetrixCdfFile Man page
getAromaUfcFile Man page
getAromaUfcFile.FragmentEquivalentClassNormalization Man page
getAromaUflFile.UflSnpInformation Man page
getAromaUgpFile.UgpGenomeInformation Man page
getAromaUnitFracBCnBinarySet Man page
getAromaUnitFracBCnBinarySet.default Man page
getAromaUnitTotalCnBinarySet Man page
getAromaUnitTotalCnBinarySet.default Man page
getArrayNames Man page
getArrayNames.AffymetrixAptSummaryFile Man page
getArraysOfInput.ArrayExplorer Man page
getAsFullCelFile Man page
getAsFullCelFile.ChipEffectFile Man page
getAsFullCelSet Man page
getAsFullCelSet.ChipEffectSet Man page
getAsteriskTags.AdditiveCovariatesNormalization Man page
getAsteriskTags.AffineCnPlm Man page
getAsteriskTags.AffinePlm Man page
getAsteriskTags.AffineSnpPlm Man page
getAsteriskTags.AlleleSummation Man page
getAsteriskTags.AllelicCrosstalkCalibration Man page
getAsteriskTags.ArrayExplorer Man page
getAsteriskTags.AvgCnPlm Man page
getAsteriskTags.AvgPlm Man page
getAsteriskTags.AvgSnpPlm Man page
getAsteriskTags.BaseCountNormalization Man page
getAsteriskTags.BasePositionNormalization Man page
getAsteriskTags.CrlmmModel Man page
getAsteriskTags.ExonRmaPlm Man page
getAsteriskTags.FirmaModel Man page
getAsteriskTags.FragmentEquivalentClassNormalization Man page
getAsteriskTags.FragmentLengthNormalization Man page
getAsteriskTags.GenericReporter Man page
getAsteriskTags.HetLogAddCnPlm Man page
getAsteriskTags.HetLogAddPlm Man page
getAsteriskTags.HetLogAddSnpPlm Man page
getAsteriskTags.LimmaBackgroundCorrection Man page
getAsteriskTags.MatNormalization Man page
getAsteriskTags.MbeiCnPlm Man page
getAsteriskTags.MbeiPlm Man page
getAsteriskTags.MbeiSnpPlm Man page
getAsteriskTags.Model Man page
getAsteriskTags.NormExpBackgroundCorrection Man page
getAsteriskTags.ProbeLevelModel Man page
getAsteriskTags.ProbeLevelTransform3 Man page
getAsteriskTags.QualityAssessmentModel Man page
getAsteriskTags.ReseqCrosstalkCalibration Man page
getAsteriskTags.RmaCnPlm Man page
getAsteriskTags.RmaPlm Man page
getAsteriskTags.RmaSnpPlm Man page
getAsteriskTags.ScaleNormalization Man page
getAsteriskTags.SmoothMultiarrayModel Man page
getAsteriskTags.SmoothRmaModel Man page
getAsteriskTags.SmoothSaModel Man page
getAsteriskTags.SnpChipEffectGroupMerge Man page
getAsteriskTags.UnitModel Man page
getAverage Man page
getAverage.AffymetrixCelSet Man page
getAverage.CnagCfhSet Man page
getAverageAsinh Man page
getAverageAsinh.AffymetrixCelSet Man page
getAverageAsinh.CnagCfhSet Man page
getAverageFile,AffymetrixCelSet-method Man page
getAverageFile,CnagCfhSet-method Man page
getAverageFile.AffymetrixCelSet Man page
getAverageFile.ChipEffectSet Man page
getAverageFile.CnChipEffectSet Man page
getAverageFile.CnagCfhSet Man page
getAverageFile.ExonChipEffectSet Man page
getAverageFile.ResidualSet Man page
getAverageFile.SnpChipEffectSet Man page
getAverageFile.WeightsSet Man page
getAverageLog Man page
getAverageLog.AffymetrixCelSet Man page
getAverageLog.CnagCfhSet Man page
getBandwidth Man page
getBandwidth.SmoothMultiarrayModel Man page
getBaseline Man page
getBaseline,ChipEffectSet-method Man page
getBaseline.ChipEffectSet Man page
getBaseline.CnChipEffectSet Man page
getBaseline.SnpChipEffectSet Man page
getBlockSizes Man page
getBlockSizes.SpatialRowColumnNormalization Man page
getCalculateResidualsFunction Man page
getCalculateResidualsFunction.AvgPlm Man page
getCalculateResidualsFunction.ProbeLevelModel Man page
getCalculateResidualsFunction.RmaPlm Man page
getCallSet Man page
getCallSet.CrlmmModel Man page
getCalls.DChipDcpFile Man page
getCdf Man page
getCdf,AffymetrixCelFile-method Man page
getCdf,AffymetrixCelSet-method Man page
getCdf,CnagCfhFile-method Man page
getCdf,CnagCfhSet-method Man page
getCdf,Model-method Man page
getCdf.AdditiveCovariatesNormalization Man page
getCdf.AffymetrixCelFile Man page
getCdf.AffymetrixCelSet Man page
getCdf.AffymetrixCnChpFile Man page
getCdf.AffymetrixCnChpSet Man page
getCdf.AffymetrixProbeTabFile Man page
getCdf.AffymetrixTsvFile Man page
getCdf.AromaUnitTabularBinaryFile Man page
getCdf.ChipEffectGroupMerge Man page
getCdf.CnagCfhFile Man page
getCdf.CnagCfhSet Man page
getCdf.FirmaModel Man page
getCdf.FragmentEquivalentClassNormalization Man page
getCdf.FragmentLengthNormalization Man page
getCdf.GcContentNormalization Man page
getCdf.Model Man page
getCdf.QualityAssessmentModel Man page
getCdf.TransformReport Man page
getCdfBin Man page
getCdfBin.DChipDcpSet Man page
getCellDim Man page
getCellDim.DChipCdfBinFile Man page
getCellIndices Man page
getCellIndices,AffymetrixCdfFile-method Man page
getCellIndices,ChipEffectFile-method Man page
getCellIndices,CnChipEffectFile-method Man page
getCellIndices,CnProbeAffinityFile-method Man page
getCellIndices,ExonChipEffectFile-method Man page
getCellIndices,ExonProbeAffinityFile-method Man page
getCellIndices,FirmaFile-method Man page
getCellIndices,ProbeAffinityFile-method Man page
getCellIndices,ResidualFile-method Man page
getCellIndices,SnpChipEffectFile-method Man page
getCellIndices,SnpProbeAffinityFile-method Man page
getCellIndices,UnitModel-method Man page
getCellIndices,WeightsFile-method Man page
getCellIndices.AffymetrixCdfFile Man page
getCellIndices.ChipEffectFile Man page
getCellIndices.ChipEffectSet Man page
getCellIndices.CnChipEffectFile Man page
getCellIndices.CnPlm Man page
getCellIndices.CnProbeAffinityFile Man page
getCellIndices.ExonChipEffectFile Man page
getCellIndices.ExonProbeAffinityFile Man page
getCellIndices.ExonRmaPlm Man page
getCellIndices.FirmaFile Man page
getCellIndices.FirmaSet Man page
getCellIndices.ProbeAffinityFile Man page
getCellIndices.ResidualFile Man page
getCellIndices.ResidualSet Man page
getCellIndices.SnpChipEffectFile Man page
getCellIndices.SnpPlm Man page
getCellIndices.SnpProbeAffinityFile Man page
getCellIndices.UnitModel Man page
getCellIndices.WeightsFile Man page
getCellIndices.WeightsSet Man page
getCellMap,ChipEffectFile-method Man page
getCellMap.ChipEffectFile Man page
getCellMapForMainCdf Man page
getCellMapForMainCdf.ChipEffectFile Man page
getCellQuartets Man page
getCellQuartets.AffymetrixCdfFile Man page
getCellsTo Man page
getCellsTo.ProbeLevelTransform3 Man page
getCellsToFit Man page
getCellsToFit.ProbeLevelTransform3 Man page
getCellsToInternal Man page
getCellsToInternal.ProbeLevelTransform3 Man page
getCellsToUpdate Man page
getCellsToUpdate.ProbeLevelTransform3 Man page
getChipEffectFileClass Man page
getChipEffectFileClass.ChipEffectSet Man page
getChipEffectFileClass.CnChipEffectSet Man page
getChipEffectFileClass.ExonChipEffectSet Man page
getChipEffectFileClass.SnpChipEffectSet Man page
getChipEffectSet Man page
getChipEffectSet,AlleleSummation-method Man page
getChipEffectSet,ProbeLevelModel-method Man page
getChipEffectSet.AlleleSummation Man page
getChipEffectSet.CnPlm Man page
getChipEffectSet.ExonRmaPlm Man page
getChipEffectSet.ProbeLevelModel Man page
getChipEffectSet.QualityAssessmentModel Man page
getChipEffectSet.SnpPlm Man page
getChipEffectSetClass Man page
getChipEffectSetClass.AlleleSummation Man page
getChipEffectSetClass.CnPlm Man page
getChipEffectSetClass.ExonRmaPlm Man page
getChipEffectSetClass.ProbeLevelModel Man page
getChipEffectSetClass.SnpPlm Man page
getChipEffects,ProbeLevelModel-method Man page
getChipEffects.ProbeLevelModel Man page
getChipType,AffymetrixCelFile-method Man page
getChipType,AffymetrixCelSet-method Man page
getChipType,CnagCfhFile-method Man page
getChipType,GenomeInformation-method Man page
getChipType,SnpInformation-method Man page
getChipType.AffymetrixAptSummaryFile Man page
getChipType.AffymetrixCdfFile Man page
getChipType.AffymetrixCelFile Man page
getChipType.AffymetrixCelSet Man page
getChipType.AffymetrixCelSetReporter Man page
getChipType.AffymetrixCnChpFile Man page
getChipType.AffymetrixPgfFile Man page
getChipType.AffymetrixProbeTabFile Man page
getChipType.AffymetrixTsvFile Man page
getChipType.AromaChipTypeAnnotationFile Man page
getChipType.CnagCfhFile Man page
getChipType.CrlmmModel Man page
getChipType.DChipCdfBinFile Man page
getChipType.DChipDcpSet Man page
getChipType.GenomeInformation Man page
getChipType.SnpInformation Man page
getChipType.UflSnpInformation Man page
getChipType.UgpGenomeInformation Man page
getChromosomeStats Man page
getChromosomeStats.GenomeInformation Man page
getChromosomes.GenomeInformation Man page
getChromosomes.UgpGenomeInformation Man page
getCnNames Man page
getCnNames,AffymetrixCdfFile-method Man page
getCnNames.AffymetrixCdfFile Man page
getColorMaps Man page
getColorMaps.ArrayExplorer Man page
getColorMaps.SpatialReporter Man page
getColumnNames.AffymetrixProbeTabFile Man page
getCombineAlleles Man page
getCombineAlleles.CnChipEffectSet Man page
getCombineAlleles.CnPlm Man page
getConfidenceScoreSet Man page
getConfidenceScoreSet.CrlmmModel Man page
getCovariates Man page
getCovariates.AdditiveCovariatesNormalization Man page
getCovariates.GcContentNormalization2 Man page
getCrlmmParametersSet Man page
getCrlmmParametersSet.CrlmmModel Man page
getCrlmmPriors Man page
getCrlmmPriors.CrlmmModel Man page
getCrlmmSNPs Man page
getCrlmmSNPs.CrlmmModel Man page
getCrlmmSNPsOnChrX Man page
getCrlmmSNPsOnChrX.CrlmmModel Man page
getCrlmmSplineParameters Man page
getCrlmmSplineParameters.CrlmmModel Man page
getData Man page
getData,AffymetrixCelFile-method Man page
getData,GenomeInformation-method Man page
getData,SnpInformation-method Man page
getData.AffymetrixCelFile Man page
getData.AffymetrixCelSet Man page
getData.AffymetrixCnChpFile Man page
getData.AffymetrixProbeTabFile Man page
getData.AffymetrixTsvFile Man page
getData.CnagCfhSet Man page
getData.GenomeInformation Man page
getData.SnpInformation Man page
getData.UflSnpInformation Man page
getData.UgpGenomeInformation Man page
getDataColumns Man page
getDataColumns.GenomeInformation Man page
getDataColumns.UflSnpInformation Man page
getDataColumns.UgpGenomeInformation Man page
getDataFlat Man page
getDataFlat.ChipEffectFile Man page
getDataFlat.FirmaFile Man page
getDataFlat.ResidualFile Man page
getDataFlat.WeightsFile Man page
getDataPairs Man page
getDataPairs.AllelicCrosstalkCalibration Man page
getDataSet Man page
getDataSet,AffymetrixCelSetReporter-method Man page
getDataSet,ArrayExplorer-method Man page
getDataSet,Model-method Man page
getDataSet.AffymetrixCelSetReporter Man page
getDataSet.ArrayExplorer Man page
getDataSet.FirmaModel Man page
getDataSet.Model Man page
getDataSet.QualityAssessmentModel Man page
getDefaultColumnNames.AromaCellMatchScoreFile Man page
getDefaultColumnNames.AromaUfcFile Man page
getDefaultExtension.AffymetrixCdfFile Man page
getDefaultExtension.AffymetrixCsvFile Man page
getDefaultExtension.AffymetrixCsvGenomeInformation Man page
getDefaultExtension.AffymetrixNetAffxCsvFile Man page
getDefaultExtension.AffymetrixPgfFile Man page
getDefaultExtension.AffymetrixTsvFile Man page
getDefaultExtension.AromaCellMatchScoreFile Man page
getDefaultExtension.AromaChipTypeAnnotationFile Man page
getDefaultFullName.AffymetrixFileSet Man page
getDefaultFullName.CnagCfhSet Man page
getDefaultSettings Man page
getDefaultSettings.AromaAffymetrix Man page
getDefaultSettings.Package Man page
getDesignMatrix Man page
getDesignMatrix.BaseCountNormalization Man page
getDesignMatrix.BasePositionNormalization Man page
getDesignMatrix.LinearModelProbeSequenceNormalization Man page
getDesignMatrix.MatNormalization Man page
getDimension Man page
getDimension.AffymetrixCdfFile Man page
getDimension.AffymetrixPgfFile Man page
getExclCells Man page
getExclCells.DChipQuantileNormalization Man page
getExclCells.QuantileNormalization Man page
getExcludes Man page
getExcludes.DChipDcpFile Man page
getExclusiveUnitSubsets Man page
getExclusiveUnitSubsets.FragmentEquivalentClassNormalization Man page
getExpandedCellMap Man page
getExpandedCellMap.ChipEffectFile Man page
getExpandedCellMap.CnChipEffectFile Man page
getExpandedCellMap.SnpChipEffectFile Man page
getExpectedOutputFullnames.MatSmoothing Man page
getExtensionPattern.AffymetrixCdfFile Man page
getExtensionPattern.AffymetrixCelFile Man page
getExtensionPattern.AffymetrixCnChpFile Man page
getExtensionPattern.AffymetrixCsvFile Man page
getExtensionPattern.AffymetrixPgfFile Man page
getExtensionPattern.AffymetrixTsvFile Man page
getExtensionPattern.AromaCellMatchScoreFile Man page
getExtensionPattern.AromaUfcFile Man page
getExtensionPattern.CnagCfhFile Man page
getExtensionPattern.DChipDcpFile Man page
getField Man page
getField.AffymetrixTsvFile Man page
getFields.SnpInformation Man page
getFields.UflSnpInformation Man page
getFileClass.FirmaSet Man page
getFileFormat Man page
getFileFormat.AffymetrixCdfFile Man page
getFileFormat.AffymetrixCelFile Man page
getFileFormat.AffymetrixCnChpFile Man page
getFileFormat.DChipCdfBinFile Man page
getFileFormat.DChipDcpFile Man page
getFileSet Man page
getFileSet.AffymetrixFileSetReporter Man page
getFileSetClass Man page
getFileSetClass.FirmaModel Man page
getFilenameExtension.AromaCellMatchScoreFile Man page
getFilenameExtension.AromaUfcFile Man page
getFilteredFragmentLengths Man page
getFilteredFragmentLengths.FragmentLengthNormalization Man page
getFirmaScores Man page
getFirmaScores,FirmaModel-method Man page
getFirmaScores.FirmaModel Man page
getFirmaSet Man page
getFirmaSet,FirmaModel-method Man page
getFirmaSet.FirmaModel Man page
getFirstCellIndices Man page
getFirstCellIndices.AffymetrixCdfFile Man page
getFirstCellPerUnitIndices Man page
getFirstCellPerUnitIndices.ExonChipEffectSet Man page
getFit Man page
getFit.BasePositionNormalization Man page
getFitSingleCellUnitFunction Man page
getFitSingleCellUnitFunction.UnitModel Man page
getFitUnitFunction Man page
getFitUnitFunction.CnPlm Man page
getFitUnitFunction.FirmaModel Man page
getFitUnitFunction.MultiArrayUnitModel Man page
getFitUnitFunction.SingleArrayUnitModel Man page
getFitUnitFunction.UnitModel Man page
getFitUnitGroupFunction Man page
getFitUnitGroupFunction,AffinePlm-method Man page
getFitUnitGroupFunction,AvgPlm-method Man page
getFitUnitGroupFunction,ExonRmaPlm-method Man page
getFitUnitGroupFunction,FirmaModel-method Man page
getFitUnitGroupFunction,HetLogAddPlm-method Man page
getFitUnitGroupFunction,MbeiPlm-method Man page
getFitUnitGroupFunction,MultiArrayUnitModel-method Man page
getFitUnitGroupFunction,RmaPlm-method Man page
getFitUnitGroupFunction,SingleArrayUnitModel-method Man page
getFitUnitGroupFunction.AffinePlm Man page
getFitUnitGroupFunction.AvgPlm Man page
getFitUnitGroupFunction.ExonRmaPlm Man page
getFitUnitGroupFunction.FirmaModel Man page
getFitUnitGroupFunction.HetLogAddPlm Man page
getFitUnitGroupFunction.MbeiPlm Man page
getFitUnitGroupFunction.MultiArrayUnitModel Man page
getFitUnitGroupFunction.RmaPlm Man page
getFitUnitGroupFunction.SingleArrayUnitModel Man page
getFitUnitGroupFunction.SmoothMultiarrayModel Man page
getFitUnitGroupFunction.SmoothRmaModel Man page
getFitUnitGroupFunction.SmoothSaModel Man page
getFragmentLengths Man page
getFragmentLengths.AffymetrixTsvFile Man page
getFragmentLengths.SnpInformation Man page
getFragmentLengths.UflSnpInformation Man page
getFragmentStarts Man page
getFragmentStarts.SnpInformation Man page
getFragmentStarts.UflSnpInformation Man page
getFragmentStops Man page
getFragmentStops.SnpInformation Man page
getFragmentStops.UflSnpInformation Man page
getFullName,Model-method Man page
getFullName,TransformReport-method Man page
getFullName.GenericReporter Man page
getFullName.Model Man page
getFullName.QualityAssessmentModel Man page
getFullName.TransformReport Man page
getFullNames.ChipEffectSetTuple Man page
getGc Man page
getGc.AffymetrixTsvFile Man page
getGcContent Man page
getGcContent.GcContentNormalization Man page
getGenomeBuild Man page
getGenomeBuild.AffymetrixNetAffxCsvFile Man page
getGenomeInformation Man page
getGenomeInformation,AffymetrixCdfFile-method Man page
getGenomeInformation.AffymetrixCdfFile Man page
getGroupDirections Man page
getGroupDirections.AffymetrixCdfFile Man page
getHeader,AffymetrixCdfFile-method Man page
getHeader,AffymetrixCelFile-method Man page
getHeader,AffymetrixPgfFile-method Man page
getHeader,AromaChipTypeAnnotationFile-method Man page
getHeader,CnagCfhFile-method Man page
getHeader.AffymetrixCdfFile Man page
getHeader.AffymetrixCelFile Man page
getHeader.AffymetrixCnChpFile Man page
getHeader.AffymetrixPgfFile Man page
getHeader.AromaChipTypeAnnotationFile Man page
getHeader.CnagCfhFile Man page
getHeader.DChipCdfBinFile Man page
getHeader.DChipDcpFile Man page
getHeaderAttributes Man page
getHeaderAttributes.AffymetrixNetAffxCsvFile Man page
getHeaderLength Man page
getHeaderLength.CnagCfhFile Man page
getHeaderV3 Man page
getHeaderV3.AffymetrixCelFile Man page
getIdentifier Man page
getIdentifier.AffymetrixCelFile Man page
getIdentifier.AffymetrixCelSet Man page
getIdentifier.AffymetrixFileSet Man page
getIdentifier.CnagCfhFile Man page
getIdentifier.CnagCfhSet Man page
getImage,AffymetrixCelFile-method Man page
getImage.AffymetrixCdfFile Man page
getImage.AffymetrixCelFile Man page
getImage.AromaUnitTabularBinaryFile Man page
getImage.ResidualFile Man page
getImage.WeightsFile Man page
getIndexToRowMap Man page
getIndexToRowMap.AffymetrixProbeTabFile Man page
getInputDataSet,TransformReport-method Man page
getInputDataSet.TransformReport Man page
getInputName Man page
getInputName.AffymetrixFileSetReporter Man page
getInputName.GenericReporter Man page
getInputTags Man page
getInputTags.AffymetrixFileSetReporter Man page
getInputTags.GenericReporter Man page
getIntensities Man page
getIntensities,AffymetrixCelSet-method Man page
getIntensities.AffymetrixCelSet Man page
getLabel.Model Man page
getListOfCdfs Man page
getListOfCdfs.AffymetrixCelSetTuple Man page
getListOfGenomeInformations Man page
getListOfGenomeInformations.ChromosomalModel Man page
getListOfPriors Man page
getListOfPriors.MultiArrayUnitModel Man page
getListOfReporters Man page
getListOfReporters.ArrayExplorer Man page
getListOfUnitNamesFiles.AffymetrixCelSetTuple Man page
getListOfUnitNamesFiles.ArrayExplorer Man page
getListOfUnitTypesFiles.AffymetrixCelSetTuple Man page
getListOfUnitTypesFiles.ArrayExplorer Man page
getMainCdf Man page
getMainCdf.AffymetrixCdfFile Man page
getMainPath.GenericReporter Man page
getMergeFunction Man page
getMergeFunction.ChipEffectGroupMerge Man page
getMergeFunction.SnpChipEffectGroupMerge Man page
getMergeGroups Man page
getMergeGroups.ExonChipEffectSet Man page
getMergeStrands Man page
getMergeStrands.SnpChipEffectSet Man page
getMergeStrands.SnpPlm Man page
getMonocellCdf Man page
getMonocellCdf.AffymetrixCdfFile Man page
getName,GenericReporter-method Man page
getName,Model-method Man page
getName,TransformReport-method Man page
getName.AffymetrixPlatform Man page
getName.FirmaModel Man page
getName.GenericReporter Man page
getName.Model Man page
getName.QualityAssessmentModel Man page
getName.TransformReport Man page
getNameOfInput.ArrayExplorer Man page
getNetAffxBuild Man page
getNetAffxBuild.AffymetrixNetAffxCsvFile Man page
getNetAffxDate Man page
getNetAffxDate.AffymetrixNetAffxCsvFile Man page
getNormalEquations Man page
getNormalEquations.LinearModelProbeSequenceNormalization Man page
getNormalizeSignalsOne Man page
getNormalizeSignalsOne.ScaleNormalization3 Man page
getNormalizeSignalsOne.UnitTypeScaleNormalization Man page
getNormalizedIntensities Man page
getNormalizedIntensities.DChipDcpFile Man page
getNumberOfFilesAveraged.CnChipEffectFile Man page
getOrderedFragmentPairMap Man page
getOrderedFragmentPairMap.AromaUfcFile Man page
getOrderedFragmentPairs Man page
getOrderedFragmentPairs.AromaUfcFile Man page
getOutputDataSet,Transform-method Man page
getOutputDataSet,TransformReport-method Man page
getOutputDataSet.Transform Man page
getOutputDataSet.TransformReport Man page
getOutputDataSet00 Man page
getOutputDataSet00.AdditiveCovariatesNormalization Man page
getOutputDataSet00.FragmentEquivalentClassNormalization Man page
getOutputDataSet00.FragmentLengthNormalization Man page
getOutputDataSet00.GcContentNormalization Man page
getOutputFiles.Transform Man page
getOutputIdentifier Man page
getOutputIdentifier.QuantileNormalization Man page
getOutputTuple Man page
getOutputTuple.SmoothMultiarrayModel Man page
getParameter Man page
getParameter.AffymetrixAptSummaryFile Man page
getParameters.AbstractProbeSequenceNormalization Man page
getParameters.AdditiveCovariatesNormalization Man page
getParameters.AllelicCrosstalkCalibration Man page
getParameters.AvgPlm Man page
getParameters.BackgroundCorrection Man page
getParameters.BaseCountNormalization Man page
getParameters.BasePositionNormalization Man page
getParameters.ChipEffectFile Man page
getParameters.ChipEffectGroupMerge Man page
getParameters.CnChipEffectFile Man page
getParameters.CnPlm Man page
getParameters.CrlmmModel Man page
getParameters.DChipQuantileNormalization Man page
getParameters.ExonChipEffectFile Man page
getParameters.ExonRmaPlm Man page
getParameters.FragmentEquivalentClassNormalization Man page
getParameters.FragmentLengthNormalization Man page
getParameters.GcContentNormalization Man page
getParameters.GcRmaBackgroundCorrection Man page
getParameters.LimmaBackgroundCorrection Man page
getParameters.MatNormalization Man page
getParameters.MatSmoothing Man page
getParameters.NormExpBackgroundCorrection Man page
getParameters.OpticalBackgroundCorrection Man page
getParameters.ProbeAffinityFile Man page
getParameters.ProbeLevelTransform3 Man page
getParameters.QuantileNormalization Man page
getParameters.ReseqCrosstalkCalibration Man page
getParameters.ResidualFile Man page
getParameters.ResidualSet Man page
getParameters.RmaBackgroundCorrection Man page
getParameters.RmaPlm Man page
getParameters.ScaleNormalization Man page
getParameters.ScaleNormalization3 Man page
getParameters.SnpChipEffectFile Man page
getParameters.SnpChipEffectGroupMerge Man page
getParameters.SnpPlm Man page
getParameters.SpatialRowColumnNormalization Man page
getParameters.UnitModel Man page
getParameters.UnitTypeScaleNormalization Man page
getParameters.WeightsFile Man page
getParameters.WeightsSet Man page
getPath,Model-method Man page
getPath,TransformReport-method Man page
getPath.AffymetrixCelSetReporter Man page
getPath.GenericReporter Man page
getPath.Model Man page
getPath.QualityAssessmentModel Man page
getPath.TransformReport Man page
getPcuTheta Man page
getPcuTheta.ChromosomalModel Man page
getPlasqTypes Man page Source code
getPlatform.AffymetrixCdfFile Man page
getPlatform.AffymetrixCelFile Man page
getPlatform.AffymetrixCelSet Man page
getPlatform.AffymetrixPgfFile Man page
getPlatform.AromaChipTypeAnnotationFile Man page
getPlatform.DChipCdfBinFile Man page
getPlatformDesign Source code
getPlatformDesignDB Man page
getPlatformDesignDB.CrlmmModel Man page
getPlm Man page
getPlm.FirmaModel Man page
getPlm.QualityAssessmentModel Man page
getPosition.AffymetrixTsvFile Man page
getPositionChipTypeUnit Man page
getPositionChipTypeUnit.ChromosomalModel Man page
getPositionChipTypeUnit.CopyNumberSegmentationModel Man page
getPositions,GenomeInformation-method Man page
getPositions.GenomeInformation Man page
getProbeAffinities,ProbeLevelModel-method Man page
getProbeAffinities.ProbeLevelModel Man page
getProbeAffinityFile Man page
getProbeAffinityFile,ProbeLevelModel-method Man page
getProbeAffinityFile.AffinePlm Man page
getProbeAffinityFile.AvgPlm Man page
getProbeAffinityFile.CnPlm Man page
getProbeAffinityFile.ExonRmaPlm Man page
getProbeAffinityFile.MbeiPlm Man page
getProbeAffinityFile.ProbeLevelModel Man page
getProbeAffinityFile.RmaPlm Man page
getProbeAffinityFile.SnpPlm Man page
getProbeSequenceData Man page
getProbeSequenceData.AffymetrixCdfFile Man page
getProbesetIds Man page
getProbesetIds.AffymetrixAptSummaryFile Man page
getQuantificationScale Man page
getQuantificationScale.AffymetrixAptSummaryFile Man page
getRawIntensities Man page
getRawIntensities.DChipDcpFile Man page
getReadArguments.AffymetrixAptSummaryFile Man page
getRectangle Man page
getRectangle.AffymetrixCelFile Man page
getReference.SpatialReporter Man page
getRegions.profileCGH Man page
getReportSet Man page
getReportSet.GenericReporter Man page
getReportSet.SpatialReporter Man page
getResidualFileClass Man page
getResidualFileClass.ResidualSet Man page
getResidualSet Man page
getResidualSet.ProbeLevelModel Man page
getResidualSetClass Man page
getResidualSetClass.ProbeLevelModel Man page
getResiduals Man page
getResiduals,QualityAssessmentModel-method Man page
getResiduals.QualityAssessmentModel Man page
getRestructor Man page
getRestructor.AffymetrixCdfFile Man page
getRlmFitFunctions Man page
getRlmFitFunctions.RmaPlm Man page
getRootPath,Model-method Man page
getRootPath.AlleleSummation Man page
getRootPath.ChipEffectTransform Man page
getRootPath.CrlmmModel Man page
getRootPath.FirmaModel Man page
getRootPath.GenericReporter Man page
getRootPath.Model Man page
getRootPath.ProbeLevelModel Man page
getRootPath.ProbeLevelTransform Man page
getRootPath.QualityAssessmentModel Man page
getRootPath.SmoothMultiarrayModel Man page
getRootPath.SmoothRmaModel Man page
getRootPath.TransformReport Man page
getSetTuple.ArrayExplorer Man page
getSetsOfProbes Man page
getSetsOfProbes.AllelicCrosstalkCalibration Man page
getSetsOfProbes.ReseqCrosstalkCalibration Man page
getSettings Man page
getSettings.Package Man page
getSignalTransform Man page
getSignalTransform.BasePositionNormalization Man page
getSignalTransform.LinearModelProbeSequenceNormalization Man page
getSnpInformation Man page
getSnpInformation.AffymetrixCdfFile Man page
getSnpNames Man page
getSnpNames,AffymetrixCdfFile-method Man page
getSnpNames.AffymetrixCdfFile Man page
getSpar Man page
getSpar.SpatialRowColumnNormalization Man page
getSteps Man page
getSteps.ASCRMAv2 Man page
getSteps.AromaPipeline Man page
getSubsetOfCellIndices Man page
getSubsetOfCellIndices.AffymetrixCdfFile Man page
getSubsetOfUnits Man page
getSubsetOfUnits.AffymetrixCdfFile Man page
getSubsetToAvg Man page
getSubsetToAvg.AllelicCrosstalkCalibration Man page
getSubsetToAvg.QuantileNormalization Man page
getSubsetToAvg.ReseqCrosstalkCalibration Man page
getSubsetToAvg.ScaleNormalization Man page
getSubsetToFit Man page
getSubsetToFit.AdditiveCovariatesNormalization Man page
getSubsetToFit.FragmentEquivalentClassNormalization Man page
getSubsetToFit.FragmentLengthNormalization Man page
getSubsetToFit.GcContentNormalization Man page
getSubsetToUpdate Man page
getSubsetToUpdate.BackgroundCorrection Man page
getSubsetToUpdate.DChipQuantileNormalization Man page
getSubsetToUpdate.QuantileNormalization Man page
getSubsetToUpdate.ScaleNormalization Man page
getSubsetToUpdate0 Man page
getSubsetToUpdate0.LimmaBackgroundCorrection Man page
getTags,GenericReporter-method Man page
getTags,Model-method Man page
getTags,TransformReport-method Man page
getTags.FirmaModel Man page
getTags.GenericReporter Man page
getTags.Model Man page
getTags.QualityAssessmentModel Man page
getTags.TransformReport Man page
getTagsOfInput.ArrayExplorer Man page
getTargetAverages Man page
getTargetAverages.FragmentEquivalentClassNormalization Man page
getTargetDistribution Man page
getTargetDistribution.QuantileNormalization Man page
getTargetDistributionIdentifier Man page
getTargetDistributionIdentifier.QuantileNormalization Man page
getTargetDistributionPathname Man page
getTargetDistributionPathname.QuantileNormalization Man page
getTargetFile Man page
getTargetFile.AbstractProbeSequenceNormalization Man page
getTargetFunction Man page
getTargetFunction.GcContentNormalization Man page
getTargetFunctions Man page
getTargetFunctions.AdditiveCovariatesNormalization Man page
getTargetFunctions.FragmentLengthNormalization Man page
getThetaStds Man page
getThetaStds.DChipDcpFile Man page
getThetas Man page
getThetas.DChipDcpFile Man page
getThetasAB Man page
getThetasAB.DChipDcpFile Man page
getTimeStamp Man page
getTimeStamp.AffymetrixAptSummaryFile Man page
getTimestamp Man page
getTimestamp,AffymetrixCelFile-method Man page
getTimestamp.AffymetrixCelFile Man page
getTimestamp.AffymetrixCnChpFile Man page
getTimestamp.CnagCfhFile Man page
getTimestamps Man page
getTimestamps.AffymetrixCelSet Man page
getTimestamps.CnagCfhSet Man page
getUniqueCdf Man page
getUniqueCdf.AffymetrixCdfFile Man page
getUnitGroupCellArrayMap Man page
getUnitGroupCellArrayMap.ChipEffectFile Man page
getUnitGroupCellChromosomePositionMap Man page
getUnitGroupCellChromosomePositionMap.AffymetrixCdfFile Man page
getUnitGroupCellChromosomePositionMap.ChipEffectFile Man page
getUnitGroupCellMap Man page
getUnitGroupCellMap,ChipEffectFile-method Man page
getUnitGroupCellMap.AffymetrixCdfFile Man page
getUnitGroupCellMap.AffymetrixCelSet Man page
getUnitGroupCellMap.ChipEffectFile Man page
getUnitGroupCellMap.FirmaFile Man page
getUnitGroupCellMap.ResidualFile Man page
getUnitGroupCellMap.WeightsFile Man page
getUnitGroupCellMapWithMonocell Man page
getUnitGroupCellMapWithMonocell.AffymetrixCdfFile Man page
getUnitGroupCellMapWithUnique Man page
getUnitGroupCellMapWithUnique.AffymetrixCdfFile Man page
getUnitGroupCellMatrixMap Man page
getUnitGroupCellMatrixMap.ChipEffectFile Man page
getUnitGroupNamesFromUgcMap Man page
getUnitGroupNamesFromUgcMap.AffymetrixCdfFile Man page
getUnitIndices Man page
getUnitIndices,GenomeInformation-method Man page
getUnitIndices.GenomeInformation Man page
getUnitIntensities Man page
getUnitIntensities,AffymetrixCelSet-method Man page
getUnitIntensities.AffymetrixCelSet Man page
getUnitNames,AffymetrixCdfFile-method Man page
getUnitNames,AffymetrixPgfFile-method Man page
getUnitNames.AffymetrixCdfFile Man page
getUnitNames.AffymetrixNetAffxCsvFile Man page
getUnitNames.AffymetrixPgfFile Man page
getUnitNames.DChipCdfBinFile Man page
getUnitNamesFile.AffymetrixCdfFile Man page
getUnitNamesFile.AffymetrixCelFile Man page
getUnitNamesFile.AffymetrixCelSet Man page
getUnitNamesFile.AffymetrixCnChpFile Man page
getUnitNamesFile.AffymetrixPgfFile Man page
getUnitNamesFile.AffymetrixPlatform Man page
getUnitNamesFile.TransformReport Man page
getUnitReadMap Man page
getUnitReadMap.AffymetrixCnChpFile Man page
getUnitSizes Man page
getUnitSizes.DChipCdfBinFile Man page
getUnitTypes,AffymetrixCdfFile-method Man page
getUnitTypes.AffymetrixCdfFile Man page
getUnitTypesFile.AffymetrixCdfFile Man page
getUnitTypesFile.AffymetrixCelFile Man page
getUnitTypesFile.AffymetrixCelSet Man page
getUnitTypesFile.AffymetrixCnChpFile Man page
getUnitTypesFile.AffymetrixPlatform Man page
getUnitTypesFile.TransformReport Man page
getUnitsOnChromosome.GenomeInformation Man page
getUnitsOnChromosome.UgpGenomeInformation Man page
getUnitsOnChromosomes.GenomeInformation Man page
getUnitsTo Man page
getUnitsTo.ProbeLevelTransform3 Man page
getUnitsToFit Man page
getUnitsToFit.CrlmmModel Man page
getUnitsToFit.ProbeLevelTransform3 Man page
getUnitsToUpdate Man page
getUnitsToUpdate.ProbeLevelTransform3 Man page
getWeights,QualityAssessmentModel-method Man page
getWeights.QualityAssessmentModel Man page
getWeightsFileClass Man page
getWeightsFileClass.WeightsSet Man page
getWeightsSet Man page
getWeightsSet.ProbeLevelModel Man page
getWeightsSetClass Man page
getWeightsSetClass.ProbeLevelModel Man page
getXAM,ChipEffectFile-method Man page
getXAM,ChipEffectSet-method Man page
getXAM.ChipEffectFile Man page
getXAM.ChipEffectSet Man page
getYY Man page
getYY.TransformReport Man page
groupUnitsByDimension Man page
groupUnitsByDimension,AffymetrixCdfFile-method Man page
groupUnitsByDimension.AffymetrixCdfFile Man page
hasAlleleBFractions.CnChipEffectFile Man page
hasAlleleBFractions.CnChipEffectSet Man page
hasAlleleBFractions.CnChipEffectSetTuple Man page
hasColumnHeader.AffymetrixProbeTabFile Man page
hasMbeiData Man page
hasMbeiData.DChipDcpFile Man page
hasNormalizedData Man page
hasNormalizedData.DChipDcpFile Man page
hasStrandiness.CnChipEffectFile Man page
hasStrandiness.CnChipEffectSet Man page
hasStrandiness.CnChipEffectSetTuple Man page
hasUnitReadMap Man page
hasUnitReadMap.AffymetrixCnChpFile Man page
hasUnitTypes Man page
hasUnitTypes.AffymetrixCdfFile Man page
highlight Man page
highlight.AffymetrixCelFile Man page
identifyCells Man page
identifyCells.AffymetrixCdfFile Man page
image270 Man page
image270,AffymetrixCelFile-method Man page
image270.AffymetrixCelFile Man page
importFrom.AromaUnitTabularBinaryFile Man page
importFromAffymetrixNetAffxCsvFile Man page
importFromAffymetrixNetAffxCsvFile.AromaUflFile Man page
importFromAffymetrixNetAffxCsvFile.AromaUgpFile Man page
importFromAffymetrixNetAffxCsvFile.AromaUnitGcContentFile Man page
importFromAffymetrixNetAffxCsvFile.AromaUnitTabularBinaryFile Man page
importFromAffymetrixProbeTabFile Man page
importFromAffymetrixProbeTabFile.AromaCellSequenceFile Man page
importFromAffymetrixTabularFile Man page
importFromAffymetrixTabularFile.AromaUfcFile Man page
importFromAffymetrixTabularFile.AromaUgpFile Man page
importFromAffymetrixTabularFile.AromaUnitTabularBinaryFile Man page
importFromApt Man page
importFromApt,CnChipEffectSet-method Man page
importFromApt.CnChipEffectSet Man page
importFromBpMap Man page
importFromBpMap.AromaCellMatchScoreFile Man page
importFromBpMap.AromaCellSequenceFile Man page
importFromDChip Man page
importFromDChip,AffymetrixCelSet-method Man page
importFromDChip,CnChipEffectSet-method Man page
importFromDChip.AffymetrixCelSet Man page
importFromDChip.CnChipEffectSet Man page
importFromDChipGenomeInformation Man page
importFromDChipGenomeInformation.AromaUnitTabularBinaryFile Man page
importFromGenericTabularFile.AromaUnitTabularBinaryFile Man page
importFromGenomeInformation Man page
importFromGenomeInformation.AromaUgpFile Man page
importFromGenomeInformation.AromaUnitTabularBinaryFile Man page
indexOfMissingSequences Man page
indexOfMissingSequences.AbstractProbeSequenceNormalization Man page
inferMmFromPm Man page
inferMmFromPm.AromaCellSequenceFile Man page
inferParameters Man page
inferParameters.CnChipEffectSet Man page
inferParameters.SnpChipEffectSet Man page
isCompatibleWithCdf Man page
isCompatibleWithCdf.GenomeInformation Man page
isCompatibleWithCdf.SnpInformation Man page
isCompatibleWithCdf.UflSnpInformation Man page
isCompatibleWithCdf.UgpGenomeInformation Man page
isDuplicated Man page
isDuplicated,AffymetrixCelSet-method Man page
isDuplicated,CnagCfhSet-method Man page
isDuplicated.AffymetrixCelSet Man page
isDuplicated.CnagCfhSet Man page
isMissing.AromaCellMatchScoreFile Man page
isMonocellCdf Man page
isMonocellCdf.AffymetrixCdfFile Man page
isPm Man page
isPm,AffymetrixCdfFile-method Man page
isPm.AffymetrixCdfFile Man page
isResequenceChip Man page
isResequenceChip,AffymetrixCdfFile-method Man page
isResequenceChip.AffymetrixCdfFile Man page
isSnpChip Man page
isSnpChip,AffymetrixCdfFile-method Man page
isSnpChip.AffymetrixCdfFile Man page
isUniqueCdf Man page
isUniqueCdf.AffymetrixCdfFile Man page
isUnitGroupCellMap Man page
isUnitGroupCellMap.data.frame Man page
isUnitGroupCellMap.default Man page
isUnitGroupCellMap.matrix Man page
justRMA Man page
justRMA.AffymetrixCelSet Man page
justRMA.default Man page
justSNPRMA Man page
justSNPRMA.AffymetrixCelSet Man page
justSNPRMA.character Man page
mapToUnitNamesFile Man page
mapToUnitNamesFile.DChipCdfBinFile Man page
mergeGroups Man page
mergeGroups.ChipEffectFile Man page
mergeStrands Man page
mergeStrands.CnChipEffectFile Man page
mergeStrands.SnpChipEffectFile Man page
migrateTool Man page
migrateTool.CopyNumberSegmentationModel Man page
nbrOfArrays,AffymetrixCelSet-method Man page
nbrOfArrays.AffymetrixAptSummaryFile Man page
nbrOfArrays.AffymetrixCelSet Man page
nbrOfArrays.AffymetrixCelSetReporter Man page
nbrOfArrays.AffymetrixCnChpSet Man page
nbrOfArrays.CnagCfhSet Man page
nbrOfArrays.DChipDcpSet Man page
nbrOfArrays.QualityAssessmentModel Man page
nbrOfArrays.TransformReport Man page
nbrOfCells.AffymetrixCdfFile Man page
nbrOfCells.AffymetrixCelFile Man page
nbrOfCells.AffymetrixPgfFile Man page
nbrOfCells.CnagCfhFile Man page
nbrOfCells.DChipCdfBinFile Man page
nbrOfCells.DChipDcpFile Man page
nbrOfCellsPerUnit Man page
nbrOfCellsPerUnit.AffymetrixCdfFile Man page
nbrOfCellsPerUnitGroup Man page
nbrOfCellsPerUnitGroup.AffymetrixCdfFile Man page
nbrOfChipTypes.ArrayExplorer Man page
nbrOfColumns.AffymetrixCdfFile Man page
nbrOfColumns.AffymetrixPgfFile Man page
nbrOfEnzymes.AromaUfcFile Man page
nbrOfEnzymes.SnpInformation Man page
nbrOfEnzymes.UflSnpInformation Man page
nbrOfGroupsPerUnit Man page
nbrOfGroupsPerUnit,AffymetrixCdfFile-method Man page
nbrOfGroupsPerUnit.AffymetrixCdfFile Man page
nbrOfQcUnits Man page
nbrOfQcUnits.AffymetrixCdfFile Man page
nbrOfRows.AffymetrixCdfFile Man page
nbrOfRows.AffymetrixPgfFile Man page
nbrOfSnps Man page
nbrOfSnps,AffymetrixCdfFile-method Man page
nbrOfSnps.AffymetrixCdfFile Man page
nbrOfSnps.CnagCfhFile Man page
nbrOfSteps Man page
nbrOfSteps.AromaPipeline Man page
nbrOfUnits.AffymetrixCdfFile Man page
nbrOfUnits.AffymetrixPgfFile Man page
nbrOfUnits.DChipCdfBinFile Man page
nbrOfUnits.DChipDcpFile Man page
nbrOfUnits.GenomeInformation Man page
nbrOfUnits.SnpInformation Man page
nbrOfUnits.UflSnpInformation Man page
nbrOfUnits.UgpGenomeInformation Man page
normalizeFragmentLength Source code
normalizeOneArrayVector Man page
normalizeOneArrayVector.FragmentEquivalentClassNormalization Man page
normalizeQuantile Man page Source code
normalizeQuantile,AffymetrixCelFile-method Man page
normalizeQuantile,AffymetrixCelSet-method Man page
normalizeQuantile.AffymetrixCelFile Man page
normalizeQuantile.AffymetrixCelSet Man page
normalizeQuantileSpline Source code
nvertMap Source code
onAttach Source code
onLoad Source code
pdInfo2Cdf Man page Source code
plasqGaussian Man page Source code
plotAllelePairs Man page
plotAllelePairs.AllelicCrosstalkCalibration Man page
plotBasepair Man page
plotBasepair.AllelicCrosstalkCalibration Man page
plotBoxplot Man page
plotBoxplot.ChipEffectSet Man page
plotBoxplotStats Man page
plotBoxplotStats.list Man page
plotCovariateEffects Man page
plotCovariateEffects.GcContentNormalization2 Man page
plotDensity Man page
plotDensity,AffymetrixCelFile-method Man page
plotDensity,AffymetrixCelSet-method Man page
plotDensity,GenomeInformation-method Man page
plotDensity.AffymetrixCelFile Man page
plotDensity.AffymetrixCelSet Man page
plotDensity.GenomeInformation Man page
plotImage Man page
plotImage,AffymetrixCelFile-method Man page
plotImage.AffymetrixCelFile Man page
plotMargins Man page
plotMargins.SpatialReporter Man page
plotMvsA Man page
plotMvsA,AffymetrixCelFile-method Man page
plotMvsA.AffymetrixCelFile Man page
plotMvsX Man page
plotMvsX,AffymetrixCelFile-method Man page
plotMvsX.AffymetrixCelFile Man page
plotNuse Man page
plotNuse.QualityAssessmentModel Man page
plotRle Man page
plotRle.QualityAssessmentModel Man page
plotXYCurve Man page
plotXYCurve.TransformReport Man page
plotXYCurveLog2 Man page
plotXYCurveLog2.TransformReport Man page
predictOne Man page
predictOne.AbstractProbeSequenceNormalization Man page
predictOne.BaseCountNormalization Man page
predictOne.LinearModelProbeSequenceNormalization Man page
predictOne.MatNormalization Man page
process,AbstractProbeSequenceNormalization-method Man page
process,AdditiveCovariatesNormalization-method Man page
process,AllelicCrosstalkCalibration-method Man page
process,ArrayExplorer-method Man page
process,BackgroundCorrection-method Man page
process,ChipEffectGroupMerge-method Man page
process,DChipQuantileNormalization-method Man page
process,FragmentEquivalentClassNormalization-method Man page
process,FragmentLengthNormalization-method Man page
process,GcContentNormalization-method Man page
process,GcRmaBackgroundCorrection-method Man page
process,GenericReporter-method Man page
process,LimmaBackgroundCorrection-method Man page
process,MatNormalization-method Man page
process,MatSmoothing-method Man page
process,OpticalBackgroundCorrection-method Man page
process,QuantileNormalization-method Man page
process,ReseqCrosstalkCalibration-method Man page
process,RmaBackgroundCorrection-method Man page
process,ScaleNormalization-method Man page
process,ScaleNormalization3-method Man page
process,SpatialReporter-method Man page
process,UnitTypeScaleNormalization-method Man page
process.AbstractProbeSequenceNormalization Man page
process.AdditiveCovariatesNormalization Man page
process.AlleleSummation Man page
process.AllelicCrosstalkCalibration Man page
process.AromaPipeline Man page
process.ArrayExplorer Man page
process.BackgroundCorrection Man page
process.ChipEffectGroupMerge Man page
process.DChipQuantileNormalization Man page
process.FragmentEquivalentClassNormalization Man page
process.FragmentLengthNormalization Man page
process.GcContentNormalization Man page
process.GcRmaBackgroundCorrection Man page
process.GenericReporter Man page
process.LimmaBackgroundCorrection Man page
process.MatNormalization Man page
process.MatSmoothing Man page
process.OpticalBackgroundCorrection Man page
process.QuantileNormalization Man page
process.ReseqCrosstalkCalibration Man page
process.RmaBackgroundCorrection Man page
process.ScaleNormalization Man page
process.ScaleNormalization3 Man page
process.SpatialReporter Man page
process.SpatialRowColumnNormalization Man page
process.UnitTypeScaleNormalization Man page
randomSeed Man page
range.AffymetrixCelFile Man page
range.AffymetrixCelSet Man page
range.CnagCfhFile Man page
range.CnagCfhSet Man page
read10K Man page
read10K.DChipSnpInformation Man page
read250K Man page
read250K.DChipSnpInformation Man page
read250KHg17 Man page
read250KHg17.DChipGenomeInformation Man page
read50K Man page
read50K.DChipSnpInformation Man page
read50KHg17 Man page
read50KHg17.DChipGenomeInformation Man page
readArrays Man page
readArrays.AffymetrixAptSummaryFile Man page
readBpmap Source code
readBpmapHeader Source code
readCcg Source code
readCcgHeader Source code
readCdf Source code
readCdfCellIndices Source code
readCdfGroupNames Source code
readCdfGroupStrands Man page Source code
readCdfHeader Source code
readCdfIsPm Source code
readCdfNbrOfCellsPerUnitGroup Source code
readCdfQc Source code
readCdfUnitNames Source code
readCdfUnits Source code
readCel Source code
readCelHeader Source code
readCelRectangle Source code
readCelUnits Source code
readCfhHeader Man page
readCfhHeader.default Man page
readCfhUnits Man page
readCfhUnits.default Man page
readCfnHeader Man page
readCfnHeader.default Man page
readCfnUnits Man page
readCfnUnits.default Man page
readDataFrame.AffymetrixCdfFile Man page
readDataFrame.AffymetrixCsvGenomeInformation Man page
readDataFrame.AffymetrixTsvFile Man page
readDataFrame.AromaUfcFile Man page
readDataFrame.DChipCdfBinFile Man page
readDataFrame.DChipGenomeInformation Man page
readDataFrame.DChipSnpInformation Man page
readDataFrame.GenomeInformation Man page
readDataFrame.SnpInformation Man page
readDataFrame.UflSnpInformation Man page
readDataFrame.UgpGenomeInformation Man page
readDataFrame2 Man page
readDataFrame2.AffymetrixProbeTabFile Man page
readDataUnitChromosomePosition Man page
readDataUnitChromosomePosition.AffymetrixNetAffxCsvFile Man page
readDataUnitFragmentLength Man page
readDataUnitFragmentLength.AffymetrixNetAffxCsvFile Man page
readGeneAssignments Man page
readGeneAssignments.AffymetrixNetAffxCsvFile Man page
readGenomeWideSNP Man page
readGenomeWideSNP.DChipGenomeInformation Man page
readHeader.AffymetrixAptSummaryFile Man page
readMatchScores Man page
readMatchScores.AromaCellMatchScoreFile Man page
readMouse430 Man page
readMouse430.DChipGenomeInformation Man page
readMouse430KenHardwired Man page
readMouse430KenHardwired.DChipGenomeInformation Man page
readParameter Man page
readParameter.CrlmmParametersFile Man page
readPgfEnv Source code
readPgfHeader Source code
readPlasqTypes Man page
readPlasqTypes.AffymetrixCdfFile Man page
readPriorsByUnits Man page
readPriorsByUnits.MultiArrayUnitModel Man page
readProbesetIds Man page
readProbesetIds.AffymetrixAptSummaryFile Man page
readRawData Man page
readRawData,AffymetrixCelFile-method Man page
readRawData.AffymetrixCelFile Man page
readRawData.AffymetrixCnChpFile Man page
readRawData.AffymetrixPgfFile Man page
readRawDataRectangle Man page
readRawDataRectangle.AffymetrixCelFile Man page
readRawDataRectangle.SpatialReporter Man page
readSequenceDataFrame Man page
readSequenceDataFrame.AffymetrixProbeTabFile Man page
readTableInternal Man page
readTableInternal.GenomeInformation Man page
readTableInternal.SnpInformation Man page
readUnitNames Man page
readUnitNames.AffymetrixNetAffxCsvFile Man page
readUnits Man page
readUnits,AffymetrixCdfFile-method Man page
readUnits,AffymetrixCelFile-method Man page
readUnits,CnagCfhFile-method Man page
readUnits,MultiArrayUnitModel-method Man page
readUnits,SingleArrayUnitModel-method Man page
readUnits.AffymetrixCdfFile Man page
readUnits.AffymetrixCelFile Man page
readUnits.AffymetrixCelSet Man page
readUnits.ChipEffectFile Man page
readUnits.ChipEffectSet Man page
readUnits.CnChipEffectFile Man page
readUnits.CnagCfhFile Man page
readUnits.CnagCfhSet Man page
readUnits.ExonChipEffectFile Man page
readUnits.FirmaFile Man page
readUnits.FirmaSet Man page
readUnits.MultiArrayUnitModel Man page
readUnits.ParameterCelFile Man page
readUnits.ProbeAffinityFile Man page
readUnits.ResidualFile Man page
readUnits.ResidualSet Man page
readUnits.SingleArrayUnitModel Man page
readUnits.SnpChipEffectFile Man page
readUnits.WeightsFile Man page
readUnits.WeightsSet Man page
readUnitsByQuartets Man page
readUnitsByQuartets,AffymetrixCdfFile-method Man page
readUnitsByQuartets.AffymetrixCdfFile Man page
rescale.AllelicCrosstalkCalibration Man page
rescaleByAll Man page
rescaleByAll.AllelicCrosstalkCalibration Man page
rescaleByAll.ReseqCrosstalkCalibration Man page
rescaleByGroups Man page
rescaleByGroups.AllelicCrosstalkCalibration Man page
restruct Man page
restruct.AffymetrixCdfFile Man page
robustSmoothSpline Source code
sampleNames Source code
seq.TransformReport Man page
setAlias,GenericReporter-method Man page
setAlias,Model-method Man page
setAlias.ArrayExplorer Man page
setAlias.GenericReporter Man page
setAlias.Model Man page
setAlias.TransformReport Man page
setArrays,ArrayExplorer-method Man page
setArrays.ArrayExplorer Man page
setBandwidth Man page
setBandwidth.SmoothMultiarrayModel Man page
setCdf Man page
setCdf,AffymetrixCelFile-method Man page
setCdf,AffymetrixCelSet-method Man page
setCdf,CnagCfhFile-method Man page
setCdf,CnagCfhSet-method Man page
setCdf.AffymetrixCelFile Man page
setCdf.AffymetrixCelSet Man page
setCdf.AffymetrixCnChpFile Man page
setCdf.AffymetrixCnChpSet Man page
setCdf.CnagCfhFile Man page
setCdf.CnagCfhSet Man page
setColorMaps Man page
setColorMaps.ArrayExplorer Man page
setColorMaps.SpatialReporter Man page
setCombineAlleles Man page
setCombineAlleles.CnChipEffectSet Man page
setCombineAlleles.CnPlm Man page
setCombineAlleles.CnProbeAffinityFile Man page
setCustomFindCdf Man page Source code
setDecodeFunction Man page
setDecodeFunction.ParameterCelFile Man page
setEncodeFunction Man page
setEncodeFunction.ParameterCelFile Man page
setGenomeInformation Man page
setGenomeInformation.AffymetrixCdfFile Man page
setLabel.Model Man page
setListOfPriors Man page
setListOfPriors.MultiArrayUnitModel Man page
setMergeFunction Man page
setMergeFunction.ChipEffectGroupMerge Man page
setMergeGroups Man page
setMergeGroups.ExonChipEffectSet Man page
setMergeGroups.ExonProbeAffinityFile Man page
setMergeGroups.ExonRmaPlm Man page
setMergeStrands Man page
setMergeStrands.SnpChipEffectSet Man page
setMergeStrands.SnpPlm Man page
setMergeStrands.SnpProbeAffinityFile Man page
setReference.SpatialReporter Man page
setRestructor Man page
setRestructor,AffymetrixCdfFile-method Man page
setRestructor.AffymetrixCdfFile Man page
setSettings Man page
setSettings.Package Man page
setSnpInformation Man page
setSnpInformation.AffymetrixCdfFile Man page
setTags,Model-method Man page
setTags.Model Man page
setUnitReadMap Man page
setUnitReadMap.AffymetrixCnChpFile Man page
setup.GenericReporter Man page
setupAromaAffymetrix Source code
setupExampleData Man page
setupExampleData,AromaAffymetrix-method Man page
setupExampleData.AromaAffymetrix Man page
smoothScatterMvsA Man page
smoothScatterMvsA,AffymetrixCelFile-method Man page
smoothScatterMvsA.AffymetrixCelFile Man page
stextChipType.AffymetrixCdfFile Man page
transformAffine Man page
transformAffine.AffymetrixCelFile Man page
transformAffine.AffymetrixCelSet Man page
translateColumnNames.AffymetrixAptSummaryFile Man page
translateColumnNames.AffymetrixProbeTabFile Man page
translateColumnNames.AffymetrixTabularFile Man page
translateFullName.AffymetrixProbeTabFile Man page
update.AromaAffymetrix Man page
update2.AffymetrixCelSet Man page
updateCel Source code
updateCelUnits Source code
updateDataFlat Man page
updateDataFlat.ChipEffectFile Man page
updateDataFlat.FirmaFile Man page
updateDataFlat.ResidualFile Man page
updateDataFlat.WeightsFile Man page
updateMatchScores Man page
updateMatchScores.AromaCellMatchScoreFile Man page
updateParameter Man page
updateParameter.CrlmmParametersFile Man page
updateSampleAnnotationSet Man page
updateSampleAnnotationSet.AffymetrixCelSet Man page
updateSettings Man page
updateSettings.Package Man page
updateSetupExplorerFile.ArrayExplorer Man page
updateUnits Man page
updateUnits,AffymetrixCelFile-method Man page
updateUnits.AffymetrixCelFile Man page
updateUnits.ChipEffectFile Man page
updateUnits.ChipEffectSet Man page
updateUnits.FirmaFile Man page
updateUnits.FirmaSet Man page
updateUnits.ParameterCelFile Man page
updateUnits.ProbeAffinityFile Man page
updateUnits.ResidualFile Man page
updateUnits.ResidualSet Man page
updateUnits.WeightsFile Man page
updateUnits.WeightsSet Man page
validate.AffymetrixCdfFile Man page
validate.AvgPlm Man page
validate.MultiArrayUnitModel Man page
verify,GenomeInformation-method Man page
verify,SnpInformation-method Man page
verify.AffymetrixCsvGenomeInformation Man page
verify.AffymetrixTsvFile Man page
verify.DChipGenomeInformation Man page
verify.DChipSnpInformation Man page
verify.GenomeInformation Man page
verify.SnpInformation Man page
verify.UflSnpInformation Man page
verify.UgpGenomeInformation Man page
writeAsFullCelFile Man page
writeAsFullCelFile.ChipEffectFile Man page
writeCNT Man page
writeCNT.SnpChipEffectFile Man page
writeCNT.SnpChipEffectSet Man page
writeCdf Man page Source code
writeCdf,AffyGenePDInfo-method Man page
writeCdf.AffyGenePDInfo Man page
writeCdf.DBPDInfo Man page
writeCdf.PDInfoList Man page
writeCdf.default Man page Source code
writeCdfByExcludingCells Man page
writeCdfByExcludingCells.AffymetrixCdfFile Man page
writeCdfHeader Source code
writeCdfQcUnits Source code
writeCdfUnits Source code
writeImage,AffymetrixCelFile-method Man page
writeImage.AffymetrixCelFile Man page
writeImage.ResidualFile Man page
writeImage.WeightsFile Man page
writeImageCombined Man page
writeImageCombined.TransformReport Man page
writeImages Man page
writeImages.SpatialReporter Man page
writeImages.TransformReport Man page
writeRegions.profileCGH Man page
writeSgr Man page
writeSgr.AffymetrixCelSet Man page
writeSignals Man page
writeSignals.ProbeLevelTransform3 Man page
writeWig Man page
writeWig.CnChipEffectSet Man page

Files

inst
inst/CITATION
inst/annotationData
inst/annotationData/genomes
inst/annotationData/genomes/Human
inst/annotationData/genomes/Human/Human,chromosomes.txt.md5
inst/annotationData/genomes/Human/Human,chromosomes.txt
inst/annotationData/samples
inst/annotationData/samples/HapMap270.saf.md5
inst/annotationData/samples/HapMap270.saf
inst/annotationData/dataSets
inst/annotationData/dataSets/HapMap,testSet
inst/annotationData/dataSets/HapMap,testSet/all,fullnames.txt.md5
inst/annotationData/dataSets/HapMap,testSet/all,fullnames.txt
inst/vignettes
inst/vignettes/replication-RMA
inst/vignettes/replication-RMA/doRMA_vs_oligo.md.rsp
inst/vignettes/replication-RMA/R
inst/vignettes/replication-RMA/R/01a.downloadAnnotationData.R
inst/vignettes/replication-RMA/R/01b.downloadRawData.R
inst/vignettes/replication-RMA/doRMA_vs_affyPLM.md.rsp
inst/vignettes/replication-RMA/justRMA_vs_affy.md.rsp
inst/vignettes/replication-MAT
inst/vignettes/replication-MAT/R
inst/vignettes/replication-MAT/R/01a.downloadAnnotationData.R
inst/vignettes/replication-MAT/R/01b.downloadRawData.R
inst/vignettes/replication-MAT/MAT_vs_oligo.md.rsp
inst/vignettes/replication-GCRMA
inst/vignettes/replication-GCRMA/R
inst/vignettes/replication-GCRMA/R/01a.downloadAnnotData.R
inst/vignettes/replication-GCRMA/R/01b.downloadRawData.R
inst/vignettes/replication-GCRMA/doGCRMA_vs_gcrma.md.rsp
inst/vignettes/CRMA,Mapping50K_Hind240,BiasCorrectedChrXY.R
inst/vignettes/CRMAv2,Mapping50K_Hind240.R
inst/vignettes/replication-CRLMM
inst/vignettes/replication-CRLMM/R
inst/vignettes/replication-CRLMM/R/01a.downloadAnnotData.R
inst/vignettes/replication-CRLMM/R/01b.downloadRawData.R
inst/vignettes/replication-CRLMM/justSNPRMA_vs_oligo.md.rsp
inst/vignettes/replication-CRLMM/CRLMM_vs_oligo.md.rsp
inst/testScripts
inst/testScripts/setup
inst/testScripts/setup/01c.installAllPackages.R
inst/testScripts/setup/spawnTests.sh
inst/testScripts/setup/99a.cleanupRootDirectories.R
inst/testScripts/setup/01a.downloadAllAnnotationData.R
inst/testScripts/setup/01b.downloadAllRawDataSet.R
inst/testScripts/annotation
inst/testScripts/annotation/chipTypes
inst/testScripts/annotation/chipTypes/GenomeWideSNP_6
inst/testScripts/annotation/chipTypes/GenomeWideSNP_6/01a.downloadAnnotationData.R
inst/testScripts/annotation/chipTypes/GenomeWideSNP_6/11.UFL.R
inst/testScripts/annotation/chipTypes/GenomeWideSNP_6/21.UGP.R
inst/testScripts/testAll.R
inst/testScripts/addons
inst/testScripts/addons/chipTypes
inst/testScripts/addons/chipTypes/Mapping50K_Hind240
inst/testScripts/addons/chipTypes/Mapping50K_Hind240/01a.downloadAnnotationData.R
inst/testScripts/addons/chipTypes/Mapping50K_Hind240/01c.installPackages.R
inst/testScripts/addons/chipTypes/Mapping50K_Hind240/01b.downloadRawData.R
inst/testScripts/addons/chipTypes/Mapping50K_Hind240/21.doACNE,seg.R
inst/testScripts/addons/chipTypes/Mapping250K_Nsp,Sty
inst/testScripts/addons/chipTypes/Mapping250K_Nsp,Sty/11.doASCRMAv2,TCNs,500K.R
inst/testScripts/addons/chipTypes/Mapping250K_Nsp,Sty/01a.downloadAnnotationData.R
inst/testScripts/addons/chipTypes/Mapping250K_Nsp,Sty/01c.installPackages.R
inst/testScripts/addons/chipTypes/Mapping250K_Nsp,Sty/01b.downloadRawData.R
inst/testScripts/addons/chipTypes/Mapping250K_Nsp
inst/testScripts/addons/chipTypes/Mapping250K_Nsp/31.doASCRMAv2,PSCBS.R
inst/testScripts/addons/chipTypes/Mapping250K_Nsp/21.doASCRMAv2,CalMaTe.R
inst/testScripts/addons/chipTypes/Mapping250K_Nsp/01a.downloadAnnotationData.R
inst/testScripts/addons/chipTypes/Mapping250K_Nsp/01c.installPackages.R
inst/testScripts/addons/chipTypes/Mapping250K_Nsp/01b.downloadRawData.R
inst/testScripts/launch.R
inst/testScripts/R
inst/testScripts/R/installUtils.R
inst/testScripts/R/downloadUtils.R
inst/testScripts/R/launchUtils.R
inst/testScripts/replication
inst/testScripts/replication/chipTypes
inst/testScripts/replication/chipTypes/GenomeWideSNP_6
inst/testScripts/replication/chipTypes/GenomeWideSNP_6/11.justSNPRMA_vs_oligo.R
inst/testScripts/replication/chipTypes/GenomeWideSNP_6/01a.downloadAnnotationData.R
inst/testScripts/replication/chipTypes/GenomeWideSNP_6/01c.installPackages.R
inst/testScripts/replication/chipTypes/GenomeWideSNP_6/01b.downloadRawData.R
inst/testScripts/replication/chipTypes/HG-U133_Plus_2
inst/testScripts/replication/chipTypes/HG-U133_Plus_2/12.doGCRMA_vs_gcrma.R
inst/testScripts/replication/chipTypes/HG-U133_Plus_2/11.doRMA_vs_affyPLM.R
inst/testScripts/replication/chipTypes/HG-U133_Plus_2/01a.downloadAnnotationData.R
inst/testScripts/replication/chipTypes/HG-U133_Plus_2/01c.installPackages.R
inst/testScripts/replication/chipTypes/HG-U133_Plus_2/01b.downloadRawData.R
inst/testScripts/replication/chipTypes/HG-U133_Plus_2/11.doRMA_vs_oligo.R
inst/testScripts/replication/chipTypes/HG-U133_Plus_2/21.justRMA_vs_affy.R
inst/testScripts/replication/chipTypes/Mapping50K_Hind240
inst/testScripts/replication/chipTypes/Mapping50K_Hind240/01a.downloadAnnotData.R
inst/testScripts/replication/chipTypes/Mapping50K_Hind240/11.justSNPRMA_vs_oligo.R
inst/testScripts/replication/chipTypes/Mapping50K_Hind240/12.CRLMM_vs_oligo.R
inst/testScripts/replication/chipTypes/Mapping50K_Hind240/01c.installPackages.R
inst/testScripts/replication/chipTypes/Mapping50K_Hind240/01b.downloadRawData.R
inst/testScripts/replication/chipTypes/Hs_PromPR_v02
inst/testScripts/replication/chipTypes/Hs_PromPR_v02/11.MatNormalization_vs_MAT.R
inst/testScripts/replication/chipTypes/Hs_PromPR_v02/01a.downloadAnnotationData.R
inst/testScripts/replication/chipTypes/Hs_PromPR_v02/01c.installPackages.R
inst/testScripts/replication/chipTypes/Hs_PromPR_v02/21.MatSmoothing_vs_MAT.R
inst/testScripts/replication/chipTypes/Hs_PromPR_v02/01b.downloadRawData.R
inst/testScripts/replication/chipTypes/Mapping250K_Nsp
inst/testScripts/replication/chipTypes/Mapping250K_Nsp/11.justSNPRMA_vs_oligo.R
inst/testScripts/replication/chipTypes/Mapping250K_Nsp/12.CRLMM_vs_oligo.R
inst/testScripts/replication/chipTypes/Mapping250K_Nsp/01a.downloadAnnotationData.R
inst/testScripts/replication/chipTypes/Mapping250K_Nsp/01c.installPackages.R
inst/testScripts/replication/chipTypes/Mapping250K_Nsp/01b.downloadRawData.R
inst/testScripts/archive
inst/testScripts/archive/system
inst/testScripts/archive/system/chipTypes
inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty
inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/31.ASCN,paired.R
inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/31.ASCN.R
inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/21.TCN,500K.R
inst/testScripts/setup.R
inst/testScripts/futures
inst/testScripts/futures/GenomeWideSNP_6
inst/testScripts/futures/GenomeWideSNP_6/01a.downloadAnnotationData.R
inst/testScripts/futures/GenomeWideSNP_6/11.BasePositionNormalization.R
inst/testScripts/futures/GenomeWideSNP_6/01b.downloadRawData.R
inst/testScripts/futures/GenomeWideSNP_6/11.AllelicCrosstalkCalibration.R
inst/testScripts/futures/HG-U133_Plus_2
inst/testScripts/futures/HG-U133_Plus_2/11.OpticalBackgroundCorrection.R
inst/testScripts/futures/HG-U133_Plus_2/12.GcRmaBackgroundCorrection.R
inst/testScripts/futures/HG-U133_Plus_2/13.RmaBackgroundCorrection.R
inst/testScripts/futures/HG-U133_Plus_2/01a.downloadAnnotationData.R
inst/testScripts/futures/HG-U133_Plus_2/14.NormExpBackgroundCorrection.R
inst/testScripts/futures/HG-U133_Plus_2/01c.installPackages.R
inst/testScripts/futures/HG-U133_Plus_2/01b.downloadRawData.R
inst/testScripts/futures/Hs_PromPR_v02
inst/testScripts/futures/Hs_PromPR_v02/11.MatNormalization.R
inst/testScripts/futures/Hs_PromPR_v02/01a.downloadAnnotationData.R
inst/testScripts/futures/Hs_PromPR_v02/01c.installPackages.R
inst/testScripts/futures/Hs_PromPR_v02/01b.downloadRawData.R
inst/testScripts/futures/Mapping10K_Xba142
inst/testScripts/futures/Mapping10K_Xba142/11.UniqueCDF.R
inst/testScripts/futures/Mapping10K_Xba142/01a.downloadAnnotationData.R
inst/testScripts/futures/Mapping10K_Xba142/11.BasePositionNormalization.R
inst/testScripts/futures/Mapping10K_Xba142/01b.downloadRawData.R
inst/testScripts/futures/Mapping10K_Xba142/11.AllelicCrosstalkCalibration.R
inst/testScripts/system
inst/testScripts/system/chipTypes
inst/testScripts/system/chipTypes/GenomeWideSNP_6
inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,plots.R
inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,GCNorm.R
inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2.R
inst/testScripts/system/chipTypes/GenomeWideSNP_6/11.justSNPRMA.R
inst/testScripts/system/chipTypes/GenomeWideSNP_6/01a.downloadAnnotationData.R
inst/testScripts/system/chipTypes/GenomeWideSNP_6/01c.installPackages.R
inst/testScripts/system/chipTypes/GenomeWideSNP_6/01b.downloadRawData.R
inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,ArrayExplorer.R
inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,extract.R
inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,AlleleSummation.R
inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,singleArray.R
inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,plotACC.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240
inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/41.BCN.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/11.RmaPlm.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/31.ASCRMA.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/42.BPN,AS.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/51.ACC,merge.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/01a.downloadAnnotData.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/42.BPN.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/21.CRMA,QA.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/61.TCN,XYbias.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/01b.downloadRawData.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/21.CRMA.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/71.doCBS,tuple.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/21.CRMA,paired.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/81.fnt.R
inst/testScripts/system/chipTypes/Test3
inst/testScripts/system/chipTypes/Test3/01a.downloadAnnotationData.R
inst/testScripts/system/chipTypes/Test3/11.ArrayExplorer.R
inst/testScripts/system/chipTypes/Test3/01d.downloadRawData.R
inst/testScripts/system/chipTypes/Test3/01c.installPackages.R
inst/testScripts/system/chipTypes/HG-U133_Plus_2
inst/testScripts/system/chipTypes/HG-U133_Plus_2/11.doRMA,ArrayExplorer.R
inst/testScripts/system/chipTypes/HG-U133_Plus_2/11.doRMA.R
inst/testScripts/system/chipTypes/HG-U133_Plus_2/11.doRMA,PLM,withPriors.R
inst/testScripts/system/chipTypes/HG-U133_Plus_2/81.doRMA,extractExpressionSet.R
inst/testScripts/system/chipTypes/HG-U133_Plus_2/21.BackgroundCorrections.R
inst/testScripts/system/chipTypes/HG-U133_Plus_2/01a.downloadAnnotationData.R
inst/testScripts/system/chipTypes/HG-U133_Plus_2/01c.installPackages.R
inst/testScripts/system/chipTypes/HG-U133_Plus_2/01b.downloadRawData.R
inst/testScripts/system/chipTypes/HG-U133_Plus_2/81.doRMA,extractAffyBatch.R
inst/testScripts/system/chipTypes/HG-U133_Plus_2/12.doGCRMA.R
inst/testScripts/system/chipTypes/CytoScanHD_Array
inst/testScripts/system/chipTypes/CytoScanHD_Array/21.doASCRMAv2,PSCN.R
inst/testScripts/system/chipTypes/CytoScanHD_Array/21,doASCRMAv2.R
inst/testScripts/system/chipTypes/CytoScanHD_Array/01a.downloadAnnotationData.R
inst/testScripts/system/chipTypes/CytoScanHD_Array/01b.downloadRawData.R
inst/testScripts/system/chipTypes/CytoScanHD_Array/21,doASCRMAv2,CBS.R
inst/testScripts/system/chipTypes/Mapping250K_Sty
inst/testScripts/system/chipTypes/Mapping250K_Sty/22.doASCRMAv2,singleArray.R
inst/testScripts/system/chipTypes/Mapping250K_Sty/21.doASCRMAv2.R
inst/testScripts/system/chipTypes/Mapping250K_Sty/01a.downloadAnnotationData.R
inst/testScripts/system/chipTypes/Mapping250K_Sty/01b.downloadRawData.R
inst/testScripts/system/chipTypes/Mapping250K_Sty/21.doASCRMAv2,ArrayExplorer.R
inst/testScripts/system/chipTypes/GenomeWideSNP_5
inst/testScripts/system/chipTypes/GenomeWideSNP_5/21.doASCRMAv2.R
inst/testScripts/system/chipTypes/GenomeWideSNP_5/01a.downloadAnnotationData.R
inst/testScripts/system/chipTypes/GenomeWideSNP_5/01b.downloadRawData.R
inst/testScripts/system/chipTypes/GenomeWideSNP_5/21.doASCRMAv2,ArrayExplorer.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240
inst/testScripts/system/chipTypes/Mapping50K_Hind240/21.doASCRMAv2.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240/11.justSNPRMA.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240/01a.downloadAnnotationData.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240/01c.installPackages.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240/01b.downloadRawData.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240/21.doASCRMAv2,ArrayExplorer.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240/10.CDF,groupUnitsBy.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240/12.justSNPRMA,CRLMM.R
inst/testScripts/system/chipTypes/Mapping50K_Hind240/21.doASCRMAv2,plotACC.R
inst/testScripts/system/chipTypes/MOUSEDIVm520650
inst/testScripts/system/chipTypes/MOUSEDIVm520650/21.doASCRMAv2.R
inst/testScripts/system/chipTypes/MOUSEDIVm520650/01a.downloadAnnotationData.R
inst/testScripts/system/chipTypes/MOUSEDIVm520650/01b.downloadRawData.R
inst/testScripts/system/chipTypes/Hs_PromPR_v02
inst/testScripts/system/chipTypes/Hs_PromPR_v02/11.MatNormalization.R
inst/testScripts/system/chipTypes/Hs_PromPR_v02/21.MatSmoothing.R
inst/testScripts/system/chipTypes/Hs_PromPR_v02/01a.downloadAnnotationData.R
inst/testScripts/system/chipTypes/Hs_PromPR_v02/01c.installPackages.R
inst/testScripts/system/chipTypes/Hs_PromPR_v02/01b.downloadRawData.R
inst/testScripts/system/chipTypes/Hs_PromPR_v02/31.AromaCellCpgFile.R
inst/testScripts/system/chipTypes/Mm_PromPR_v02
inst/testScripts/system/chipTypes/Mm_PromPR_v02/10,CDF,unique.R
inst/testScripts/system/chipTypes/Mm_PromPR_v02/01a.downloadAnnotationData.R
inst/testScripts/system/chipTypes/MoEx-1_0-st-v1
inst/testScripts/system/chipTypes/MoEx-1_0-st-v1/11.GcRmaBackgroundCorrection.R
inst/testScripts/system/chipTypes/MoEx-1_0-st-v1/01a.downloadAnnotationData.R
inst/testScripts/system/chipTypes/MoEx-1_0-st-v1/01b.downloadRawData.R
inst/testScripts/system/chipTypes/MoGene-1_0-st-v1
inst/testScripts/system/chipTypes/MoGene-1_0-st-v1/12.QuantileNormalization.R
inst/testScripts/system/chipTypes/MoGene-1_0-st-v1/11.RmaBackgroundCorrection.R
inst/testScripts/system/chipTypes/MoGene-1_0-st-v1/01a.downloadAnnotationData.R
inst/testScripts/system/chipTypes/MoGene-1_0-st-v1/01b.downloadRawData.R
inst/testScripts/system/chipTypes/HuEx-1_0-st-v2
inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/01b.downloadRawData,GEO.R
inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/test20101202,gcrma.R
inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/01a.downloadAnnotationData.R
inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/21.doFIRMA,extras.R
inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/01b.downloadRawData.R
inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/21.doFIRMA.R
inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/21.doFIRMA,QC.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142
inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,plotACC.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,plots,pairs.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/31.ACC,mergeShifts.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,singleArray.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,PSCN.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,FLN,zero.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,CBS.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/11.doCRMAv1.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,CBS,CE.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,HaarSeg.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/11.doCRMAv1,SmNorm.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,extractAndWrite.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,QA.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/01a.downloadAnnotationData.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/01c.installPackages.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/31.doASCRMAv1.ArrayExplorer.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,extract.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,CBS,any.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/41.ACC,expectile.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/01b.downloadRawData.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/31.ACC,BCN.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,TotalFreqB.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,plots.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/12.doASCRMAv1.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,CBS,ref.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,GLAD.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/10.CDF,groupUnitsBy.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142/10.CDF,readDataFrame.R
inst/testScripts/system/chipTypes/Mapping250K_Nsp
inst/testScripts/system/chipTypes/Mapping250K_Nsp/21.doASCRMAv1,ArrayExplorer.R
inst/testScripts/system/chipTypes/Mapping250K_Nsp/01a.downloadAnnotationData.R
inst/testScripts/system/chipTypes/Mapping250K_Nsp/31.doASCRMAv2.R
inst/testScripts/system/chipTypes/Mapping250K_Nsp/01b.downloadRawData.R
inst/testScripts/system/chipTypes/Mapping250K_Nsp/31.doASCRMAv2,TumorNormalPair.R
inst/testScripts/system/chipTypes/Cytogenetics_Array
inst/testScripts/system/chipTypes/Cytogenetics_Array/test20090828,cyto.R
inst/testScripts/system/chipTypes/Cytogenetics_Array/01a.downloadAnnotationData.R
inst/testScripts/system/chipTypes/Cytogenetics_Array/01b.downloadRawData.R
inst/testScripts/complete
inst/testScripts/complete/dataSets
inst/testScripts/complete/dataSets/GSE27691
inst/testScripts/complete/dataSets/GSE27691/21.doASCRMAv2.R
inst/testScripts/complete/dataSets/GSE27691/01a.downloadAnnotationData.R
inst/testScripts/complete/dataSets/GSE27691/01c.installPackages.R
inst/testScripts/complete/dataSets/GSE27691/01b.downloadRawData.R
inst/testScripts/complete/dataSets/GSE12702
inst/testScripts/complete/dataSets/GSE12702/22.doASCRMAv2,CalMaTe,Nsp.R
inst/testScripts/complete/dataSets/GSE12702/11.doASCRMAv2,Sty.R
inst/testScripts/complete/dataSets/GSE12702/31.doASCRMAv2,PairedPSCBS,Sty.R
inst/testScripts/complete/dataSets/GSE12702/32.doASCRMAv2,CalMaTe,PairedPSCBS,Sty.R
inst/testScripts/complete/dataSets/GSE12702/31.doASCRMAv2,PairedPSCBS,Nsp.R
inst/testScripts/complete/dataSets/GSE12702/32.doASCRMAv2,CalMaTe,PairedPSCBS,Nsp.R
inst/testScripts/complete/dataSets/GSE12702/11.doASCRMAv2,Nsp.R
inst/testScripts/complete/dataSets/GSE12702/01a.downloadAnnotationData.R
inst/testScripts/complete/dataSets/GSE12702/01c.installPackages.R
inst/testScripts/complete/dataSets/GSE12702/22.doASCRMAv2,CalMaTe,Sty.R
inst/testScripts/complete/dataSets/GSE12702/01b.downloadRawData.R
inst/testScripts/complete/dataSets/GSE12702/GSE12702,samples.txt
inst/testScripts/complete/dataSets/GSE13372
inst/testScripts/complete/dataSets/GSE13372/GSE13372,samples.txt
inst/testScripts/complete/dataSets/GSE13372/22.doASCRMAv2,CalMaTe.R
inst/testScripts/complete/dataSets/GSE13372/31.doASCRMAv2,PairedPSCBS.R
inst/testScripts/complete/dataSets/GSE13372/32.doASCRMAv2,CalMaTe,PairedPSCBS.R
inst/testScripts/complete/dataSets/GSE13372/21.doASCRMAv2.R
inst/testScripts/complete/dataSets/GSE13372/01a.downloadAnnotationData.R
inst/testScripts/complete/dataSets/GSE13372/01c.installPackages.R
inst/testScripts/complete/dataSets/GSE13372/01b.downloadRawData.R
inst/testScripts/complete/dataSets/GSE19539
inst/testScripts/complete/dataSets/GSE19539/22.doASCRMAv2,CalMaTe.R
inst/testScripts/complete/dataSets/GSE19539/21.doASCRMAv2.R
inst/testScripts/complete/dataSets/GSE19539/01a.downloadAnnotationData.R
inst/testScripts/complete/dataSets/GSE19539/01c.installPackages.R
inst/testScripts/complete/dataSets/GSE19539/01b.downloadRawData.R
inst/testScripts/complete/dataSets/GSE20584
inst/testScripts/complete/dataSets/GSE20584/GSE20584,samples.txt
inst/testScripts/complete/dataSets/GSE20584/31.doASCRMAv2,PairedPSCBS.R
inst/testScripts/complete/dataSets/GSE20584/21.doASCRMAv2.R
inst/testScripts/complete/dataSets/GSE20584/01a.downloadAnnotationData.R
inst/testScripts/complete/dataSets/GSE20584/01c.installPackages.R
inst/testScripts/complete/dataSets/GSE20584/01b.downloadRawData.R
inst/testScripts/complete/dataSets/GSE34754
inst/testScripts/complete/dataSets/GSE34754/GSE34754,samples.txt
inst/testScripts/complete/dataSets/GSE34754/22.doASCRMAv2,CalMaTe.R
inst/testScripts/complete/dataSets/GSE34754/31.doASCRMAv2,PairedPSCBS.R
inst/testScripts/complete/dataSets/GSE34754/32.doASCRMAv2,CalMaTe,PairedPSCBS.R
inst/testScripts/complete/dataSets/GSE34754/21.doASCRMAv2.R
inst/testScripts/complete/dataSets/GSE34754/01a.downloadAnnotationData.R
inst/testScripts/complete/dataSets/GSE34754/01c.installPackages.R
inst/testScripts/complete/dataSets/GSE34754/01b.downloadRawData.R
inst/testScripts/robustness
inst/testScripts/robustness/chipTypes
inst/testScripts/robustness/chipTypes/Mapping50K_Hind240
inst/testScripts/robustness/chipTypes/Mapping50K_Hind240/01a.downloadAnnotData.R
inst/testScripts/robustness/chipTypes/Mapping50K_Hind240/01b.downloadRawData.R
inst/testScripts/robustness/chipTypes/Mapping50K_Hind240/21.doASCRMAv2,CRLMM.R
inst/testScripts/robustness/chipTypes/MoGene-1_0-st-v1
inst/testScripts/robustness/chipTypes/MoGene-1_0-st-v1/11.GcRmaBgCorr.R
inst/testScripts/robustness/chipTypes/MoGene-1_0-st-v1/01a.downloadAnnotationData.R
inst/testScripts/robustness/chipTypes/MoGene-1_0-st-v1/01b.downloadRawData.R
inst/testScripts/robustness/chipTypes/Mapping10K_Xba142
inst/testScripts/robustness/chipTypes/Mapping10K_Xba142/01a.downloadAnnotData.R
inst/testScripts/robustness/chipTypes/Mapping10K_Xba142/11.doASCRMAv1,CBS,invalid.R
inst/testScripts/robustness/chipTypes/Mapping10K_Xba142/01b.downloadRawData.R
inst/downloadScripts
inst/downloadScripts/chipTypes
inst/downloadScripts/chipTypes/Mapping50K_Hind240,Xba240
inst/downloadScripts/chipTypes/Mapping50K_Hind240,Xba240/HapMap,testSet,100K.R
inst/buildScripts
inst/buildScripts/chipTypes
inst/buildScripts/chipTypes/GenomeWideSNP_6
inst/buildScripts/chipTypes/GenomeWideSNP_6/na31
inst/buildScripts/chipTypes/GenomeWideSNP_6/na31/GenomeWideSNP_6,UGP.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na31/GenomeWideSNP_6,default,UGP+UFL.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na31/GenomeWideSNP_6,UFL.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,UGP.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na32
inst/buildScripts/chipTypes/GenomeWideSNP_6/na32/GenomeWideSNP_6,UGP.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na32/GenomeWideSNP_6,default,UGP+UFL.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na32/GenomeWideSNP_6,UFL.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na33
inst/buildScripts/chipTypes/GenomeWideSNP_6/na33/GenomeWideSNP_6,UGP.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na33/GenomeWideSNP_6,default,UGP+UFL.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na33/GenomeWideSNP_6,UFL.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,default,UGP+UFL.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,UFL.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na26
inst/buildScripts/chipTypes/GenomeWideSNP_6/na26/GenomeWideSNP_6,UFL,na26.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na26/GenomeWideSNP_6,UGP,na26.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na26/GWS6,default,UGP+UFL,na26.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na27.1
inst/buildScripts/chipTypes/GenomeWideSNP_6/na27.1/GenomeWideSNP_6,UGP,na27.1.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na27.1/GenomeWideSNP_6,UFL,na27.1.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na27.1/GWS6,default,UGP+UFL,na27.1.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na35
inst/buildScripts/chipTypes/GenomeWideSNP_6/na35/3.GenomeWideSNP_6,default.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na35/2.GenomeWideSNP_6,UFL.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na35/1.GenomeWideSNP_6,UGP.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na25
inst/buildScripts/chipTypes/GenomeWideSNP_6/na25/GenomeWideSNP_6,UFL,na25.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na27
inst/buildScripts/chipTypes/GenomeWideSNP_6/na27/GenomeWideSNP_6,UGC,na27.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na30
inst/buildScripts/chipTypes/GenomeWideSNP_6/na30/GenomeWideSNP_6,UGP,na30.R
inst/buildScripts/chipTypes/GenomeWideSNP_6/na30/GenomeWideSNP_6,UFL,na30.R
inst/buildScripts/chipTypes/Mapping50K_Xba240
inst/buildScripts/chipTypes/Mapping50K_Xba240/Mapping50K_Xba240,ACS.R
inst/buildScripts/chipTypes/Mapping50K_Xba240/Mapping50K_Xba240,UFL.R
inst/buildScripts/chipTypes/Mapping50K_Xba240/Mapping50K_Xba240,UGP.R
inst/buildScripts/chipTypes/Mapping50K_Xba240/na26
inst/buildScripts/chipTypes/Mapping50K_Xba240/na26/Mapping50K_Xba240,UGP,na26.R
inst/buildScripts/chipTypes/Mapping50K_Xba240/na26/Mapping50K_Xba240,UFL,na26.R
inst/buildScripts/chipTypes/HG-Focus
inst/buildScripts/chipTypes/HG-Focus/HG-Focus,ACS.R
inst/buildScripts/chipTypes/HG-U133A
inst/buildScripts/chipTypes/HG-U133A/HG-U133A,ACS.R
inst/buildScripts/chipTypes/CytoScanHD_Array
inst/buildScripts/chipTypes/CytoScanHD_Array/na32
inst/buildScripts/chipTypes/CytoScanHD_Array/na32/CytoScanHD_Array,UGP.R
inst/buildScripts/chipTypes/CytoScanHD_Array/na32/CytoScanHD_Array,UFL.R
inst/buildScripts/chipTypes/CytoScanHD_Array/CytoScanHD_Array,ACS.R
inst/buildScripts/chipTypes/Mapping250K_Sty
inst/buildScripts/chipTypes/Mapping250K_Sty/na31
inst/buildScripts/chipTypes/Mapping250K_Sty/na31/Mapping250K_Sty,UGP,na31.R
inst/buildScripts/chipTypes/Mapping250K_Sty/na31/Mapping250K_Sty,UFL,na31.R
inst/buildScripts/chipTypes/Mapping250K_Sty/na28
inst/buildScripts/chipTypes/Mapping250K_Sty/na28/Mapping250K_Sty,UGC,na28.R
inst/buildScripts/chipTypes/Mapping250K_Sty/na26
inst/buildScripts/chipTypes/Mapping250K_Sty/na26/Mapping250K_Sty,UFL,na26.R
inst/buildScripts/chipTypes/Mapping250K_Sty/na26/Mapping250K_Sty,UGP,na26.R
inst/buildScripts/chipTypes/GenomeWideSNP_5
inst/buildScripts/chipTypes/GenomeWideSNP_5/na26
inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GWS5,default,UGP+UFL,na26.R
inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GenomeWideSNP_5,UFL,na26.R
inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GenomeWideSNP_5,UFL,na26,GWS6.R
inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GenomeWideSNP_5,UGP,na26.R
inst/buildScripts/chipTypes/GenomeWideSNP_5/na25
inst/buildScripts/chipTypes/GenomeWideSNP_5/na25/GenomeWideSNP_5,UFL,na25,GWS6.R
inst/buildScripts/chipTypes/Canine_2
inst/buildScripts/chipTypes/Canine_2/Canine_2,ACS.R
inst/buildScripts/chipTypes/Mapping50K_Hind240
inst/buildScripts/chipTypes/Mapping50K_Hind240/Mapping50K_Hind240,UFL.R
inst/buildScripts/chipTypes/Mapping50K_Hind240/Mapping50K_Xba240,UGP.R
inst/buildScripts/chipTypes/Mapping50K_Hind240/na26
inst/buildScripts/chipTypes/Mapping50K_Hind240/na26/Mapping50K_Hind240,UFL,na26.R
inst/buildScripts/chipTypes/Mapping50K_Hind240/na26/Mapping50K_Hind240,UGP,na26.R
inst/buildScripts/chipTypes/MOUSEDIVm520650
inst/buildScripts/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650,ACS.R
inst/buildScripts/chipTypes/MOUSEDIVm520650/na30
inst/buildScripts/chipTypes/MOUSEDIVm520650/na30/MOUSEDIVm520650,UGP,na30.R
inst/buildScripts/chipTypes/MOUSEDIVm520650/na30/MOUSEDIVm520650,UFL,na30.R
inst/buildScripts/chipTypes/DogSty06m520431
inst/buildScripts/chipTypes/DogSty06m520431/DogSty06m520431,ACS.R
inst/buildScripts/chipTypes/HuGene-1_0-st-v1
inst/buildScripts/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,NetAffx.R
inst/buildScripts/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,ACS.R
inst/buildScripts/chipTypes/MoGene-1_0-st-v1
inst/buildScripts/chipTypes/MoGene-1_0-st-v1/MoGene-1_0-st-v1,ACS.R
inst/buildScripts/chipTypes/MoGene-1_0-st-v1/MoGene-1_0-st-v1,ACP.R
inst/buildScripts/chipTypes/MoGene-1_0-st-v1/MoGene-1_0-st-v1,UGP.R
inst/buildScripts/chipTypes/HuEx-1_0-st-v2
inst/buildScripts/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2,CDF,exonByTranscript.R
inst/buildScripts/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2,ACS.R
inst/buildScripts/chipTypes/Mapping10K_Xba142
inst/buildScripts/chipTypes/Mapping10K_Xba142/Mapping10K_Xba142,ACS.R
inst/buildScripts/chipTypes/Mapping10K_Xba142/na26
inst/buildScripts/chipTypes/Mapping10K_Xba142/na26/Mapping10K_Xba142,UFL,na26.R
inst/buildScripts/chipTypes/Mapping10K_Xba142/na26/Mapping10K_Xba142,UGP,na26.R
inst/buildScripts/chipTypes/Mapping250K_Nsp
inst/buildScripts/chipTypes/Mapping250K_Nsp/na31
inst/buildScripts/chipTypes/Mapping250K_Nsp/na31/Mapping250K_Nsp,UFL,na31.R
inst/buildScripts/chipTypes/Mapping250K_Nsp/na31/Mapping250K_Nsp,UGP,na31.R
inst/buildScripts/chipTypes/Mapping250K_Nsp/na28
inst/buildScripts/chipTypes/Mapping250K_Nsp/na28/Mapping250K_Nsp,UGC,na28.R
inst/buildScripts/chipTypes/Mapping250K_Nsp/na26
inst/buildScripts/chipTypes/Mapping250K_Nsp/na26/Mapping250K_Nsp,UFL,na26.R
inst/buildScripts/chipTypes/Mapping250K_Nsp/na26/Mapping250K_Nsp,UGP,na26.R
inst/buildScripts/chipTypes/Cytogenetics_Array
inst/buildScripts/chipTypes/Cytogenetics_Array/na28
inst/buildScripts/chipTypes/Cytogenetics_Array/na28/Cytogenetics_Array,UGP,na28.R
inst/buildScripts/chipTypes/Cytogenetics_Array/Cytogenetics_Array,ACS.R
inst/buildScripts/chipTypes/Mapping10K_Xba131
inst/buildScripts/chipTypes/Mapping10K_Xba131/na26
inst/buildScripts/chipTypes/Mapping10K_Xba131/na26/Mapping10K_Xba131,UFL,na26.R
inst/buildScripts/chipTypes/Mapping10K_Xba131/na26/Mapping10K_Xba131,UGP,na26.R
inst/buildScripts/chipTypes/Mapping10K_Xba131/Mapping10K_Xba131,ACS.R
tests
tests/AffymetrixCdfFile.R
tests/AffymetrixCelSet.R
tests/AffymetrixCelFile.R
tests/002.setupExampleData,rawData.R
tests/001.setupExampleData,annotationData.R
NAMESPACE
NEWS
R
R/ProbeLevelTransform.R
R/QualityAssessmentFile.R
R/BackgroundCorrection.R
R/ProbeLevelModel.calculateResiduals.R
R/LimmaBackgroundCorrection.R
R/SnpProbeAffinityFile.R
R/ResidualFile.R
R/SnpChipEffectFile.R
R/DChipCdfBinFile.R
R/CnChipEffectSet.importFromDChip.R
R/AffinePlm.R
R/GenomeInformation.AFFX.R
R/SingleArrayUnitModel.R
R/SnpPlm.R
R/ReseqCrosstalkCalibration.R
R/AffymetrixFileSetReporter.R
R/AffymetrixCelFile.extractMatrix.R
R/AffymetrixCelFile.BG.R
R/ProbeLevelModel.fit.R
R/AffymetrixCdfFile.MONOCELL.R
R/isUnitGroupCellMap.R
R/DChipDcpFile.R
R/AffymetrixPlatform.R
R/ParameterCelSet.R
R/AffymetrixCelSet.BG.R
R/CnagCfhFile.R
R/AffymetrixProbeTabFile.R
R/ChipEffectSet.PLOT.R
R/CnChipEffectFile.R
R/ChipEffectGroupMerge.R
R/021.dynamic_imports.R
R/GenomeInformation.R
R/QualityAssessmentSet.R
R/AromaCellMatchScoreFile.R
R/000.R
R/SnpCnvQSet.extractTheta.R
R/AffymetrixCdfFile.readDataFrame.R
R/AllelicCrosstalkCalibration.getSetsOfProbes.R
R/createExonByTranscriptCdf.R
R/ChipEffectSetTuple.R
R/UnitModel.R
R/AffymetrixCelSetReporter.R
R/AllelicCrosstalkCalibration.R
R/WeightsFile.R
R/AbstractProbeSequenceNormalization.R
R/AffymetrixCelSet.extractMatrix.R
R/AromaUnitTabularBinaryFile.AFFX.PLOT.R
R/SingleArrayUnitModel.fit.R
R/UflSnpInformation.R
R/SmoothMultiarrayModel.R
R/ChipEffectSet.getBaseline.R
R/FirmaSet.R
R/AffymetrixCsvFile.R
R/doCRMAv1.R
R/AffymetrixCdfFile.R
R/AromaUfcFile.R
R/QuantileNormalization.xtra.R
R/AffymetrixCdfFile.SNPs.R
R/AromaCellPositionFile.AFFX.R
R/AllelicCrosstalkCalibration.PLOT.R
R/ChipEffectFile.fromDataFile.R
R/AffymetrixAptSummaryFile.R
R/AromaUnitTabularBinaryFile.AFFX.R
R/AffymetrixCelSet.R
R/AffymetrixCelFile.PLOT.R
R/ASCRMAv2.R
R/HetLogAddCnPlm.R
R/ProbeLevelTransform3.R
R/AromaUnitGcContentFile.AFFX.R
R/AffymetrixCdfFile.getAlleleCellPairs.R
R/profileCGH.getRegions.R
R/readCdfGroupStrands.R
R/SnpQSet.extractTheta.R
R/DChipCdfBinFile.mapToUnitNamesFile.R
R/SmoothSaModel.R
R/AromaPipeline.R
R/AffymetrixNetAffxCsvFile.XTRS.R
R/OpticalBackgroundCorrection.R
R/ChipEffectSet.calculateBaseline.R
R/999.DEPRECATED.R
R/bpmapCluster2Cdf.R
R/MatNormalization.R
R/AffymetrixCdfFile.COUNTS.R
R/ExonProbeAffinityFile.R
R/CnChipEffectSet.importFromApt.R
R/AffymetrixCelSetTuple.R
R/009.setup.R
R/GenericReporter.R
R/Model.R
R/AffymetrixCelSet.getAverageFile.R
R/findByCdf2.R
R/ChipEffectFile.R
R/CrlmmParametersFile.R
R/MbeiSnpPlm.R
R/AffymetrixCelFile.normalizeAffine.R
R/SnpChipEffectSet.extractTotalAndFreqB.R
R/CnChipEffectSetTuple.R
R/profileCGH.writeRegions.R
R/ChipEffectSet.TOFULL.R
R/DChipDcpSet.extras.R
R/plotBoxplotStats.list.R
R/TransformReport.R
R/CnChipEffectSet.R
R/UnitModel.fitCnProbes.R
R/AvgCnPlm.R
R/randomSeed.R
R/AdditiveCovariatesNormalization.R
R/AvgSnpPlm.R
R/ScaleNormalization3.R
R/AffymetrixCdfFile.getProbeSequenceData.R
R/AffymetrixCnChpSet.R
R/ChipEffectSet.extractExpressionSet.R
R/ExonRmaPlm.R
R/readCfnHeader.R
R/DChipDcpSet.R
R/AffymetrixCelSet.extractFeatureSet.R
R/fitPlasqUnit.R
R/setupExampleData.R
R/SpatialReporter.R
R/AffymetrixCdfFile.UNIQUE.R
R/WeightsSet.R
R/SnpChipEffectNnn.writeCNT.R
R/CnagCfhSet.R
R/SmoothRmaModel.R
R/AffymetrixCelFile.normalizeQuantile.R
R/MbeiCnPlm.R
R/MultiArrayUnitModel.R
R/AffymetrixCelFile.R
R/AffymetrixCelSet.extractAffyBatch.R
R/AffymetrixCelSet.justSNPRMA.R
R/MatSmoothing.R
R/readCfnUnits.R
R/QuantileNormalization.R
R/CnPlm.R
R/ChipEffectFile.getUnitGroupCellMatrixMap.R
R/HetLogAddPlm.R
R/AffymetrixCelSet.importFromDChip.R
R/doCRMAv2.R
R/AffymetrixCelFile.fitQuantileNormFcn.R
R/doFIRMA.R
R/RmaPlm.R
R/AromaUgpFile.AFFX.R
R/Package.XTRA.R
R/pdInfo2Cdf.R
R/SnpChipEffectSet.R
R/SnpChipEffectSet.extractSnpQSet.R
R/CrlmmParametersSet.R
R/AffymetrixCdfFile.getAlleleProbePairs3.R
R/AffyGenePDInfo.writeCdf.R
R/AromaCellCpgFile.AFFX.R
R/justRMA.R
R/ExonChipEffectSet.R
R/GcContentNormalization2.plotCovariateEffects.R
R/ChromosomalModel.AFFX.R
R/ResidualSet.R
R/ChipEffectSet.R
R/SmoothMultiarrayModel.fit.R
R/CopyNumberChromosomalModel.applyCCF.R
R/ChipEffectFile.xam.R
R/CrlmmModel.EXT.R
R/env2Cdf.R
R/ExonRmaPlm.calculateWeights.R
R/AffymetrixCelSet.writeSgr.R
R/FragmentEquivalentClassNormalization.R
R/AffymetrixCdfFile.getCellQuartets.R
R/MbeiPlm.R
R/AffymetrixCdfFile.getUnitGroupNamesFromUgcMap.R
R/AffineCnPlm.R
R/readCfhUnits.R
R/AffymetrixCdfFile.getSubsetOfCellIndices.R
R/AromaCellMatchScoreFile.AFFX.R
R/GcContentNormalization2.R
R/AffymetrixCelSet.PLOT.R
R/AffymetrixFileSet.getIdentifier.R
R/SnpChipEffectFile.extractTotalAndFracB.R
R/AffymetrixTabularFile.R
R/dropCellsFromCdfList.R
R/UgpGenomeInformation.R
R/SnpChipEffectSet.extractAlleleSet.R
R/CnProbeAffinityFile.R
R/SpatialRowColumnNormalization.R
R/SnpChipEffectSet.extractSnpCnvQSet.R
R/QualityAssessmentModel.R
R/DChipGenomeInformation.R
R/AffymetrixCdfFile.PLOT.R
R/ArrayExplorer.R
R/readCfhHeader.R
R/ChipEffectSet.extractTheta.R
R/FirmaModel.R
R/AvgPlm.R
R/SnpInformation.R
R/LinearModelProbeSequenceNormalization.R
R/Transform.R
R/ParameterCelFile.R
R/doGCRMA.R
R/AffymetrixCdfFile.getAlleleProbePairs2.R
R/AffymetrixCdfFile.writeCdfByExcludingCells.R
R/006.fixVarArgs.R
R/ChipEffectTransform.R
R/ProbeLevelModel.calculateWeights.R
R/AffymetrixPgfFile.R
R/DChipSnpInformation.R