aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

Share:

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.

Author
Henrik Bengtsson [aut, cre, cph], James Bullard [ctb], Kasper Hansen [ctb], Pierre Neuvial [ctb], Elizabeth Purdom [ctb], Mark Robinson [ctb], Ken Simpson [ctb]
Date of publication
2016-01-10 00:00:03
Maintainer
Henrik Bengtsson <henrikb@braju.com>
License
LGPL (>= 2.1)
Version
3.0.0
URLs

View on CRAN

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

Files in this package

aroma.affymetrix
aroma.affymetrix/inst
aroma.affymetrix/inst/CITATION
aroma.affymetrix/inst/annotationData
aroma.affymetrix/inst/annotationData/genomes
aroma.affymetrix/inst/annotationData/genomes/Human
aroma.affymetrix/inst/annotationData/genomes/Human/Human,chromosomes.txt.md5
aroma.affymetrix/inst/annotationData/genomes/Human/Human,chromosomes.txt
aroma.affymetrix/inst/annotationData/samples
aroma.affymetrix/inst/annotationData/samples/HapMap270.saf.md5
aroma.affymetrix/inst/annotationData/samples/HapMap270.saf
aroma.affymetrix/inst/annotationData/dataSets
aroma.affymetrix/inst/annotationData/dataSets/HapMap,testSet
aroma.affymetrix/inst/annotationData/dataSets/HapMap,testSet/all,fullnames.txt.md5
aroma.affymetrix/inst/annotationData/dataSets/HapMap,testSet/all,fullnames.txt
aroma.affymetrix/inst/vignettes
aroma.affymetrix/inst/vignettes/replication-RMA
aroma.affymetrix/inst/vignettes/replication-RMA/doRMA_vs_oligo.md.rsp
aroma.affymetrix/inst/vignettes/replication-RMA/R
aroma.affymetrix/inst/vignettes/replication-RMA/R/01a.downloadAnnotationData.R
aroma.affymetrix/inst/vignettes/replication-RMA/R/01b.downloadRawData.R
aroma.affymetrix/inst/vignettes/replication-RMA/doRMA_vs_affyPLM.md.rsp
aroma.affymetrix/inst/vignettes/replication-RMA/justRMA_vs_affy.md.rsp
aroma.affymetrix/inst/vignettes/replication-MAT
aroma.affymetrix/inst/vignettes/replication-MAT/R
aroma.affymetrix/inst/vignettes/replication-MAT/R/01a.downloadAnnotationData.R
aroma.affymetrix/inst/vignettes/replication-MAT/R/01b.downloadRawData.R
aroma.affymetrix/inst/vignettes/replication-MAT/MAT_vs_oligo.md.rsp
aroma.affymetrix/inst/vignettes/replication-GCRMA
aroma.affymetrix/inst/vignettes/replication-GCRMA/R
aroma.affymetrix/inst/vignettes/replication-GCRMA/R/01a.downloadAnnotData.R
aroma.affymetrix/inst/vignettes/replication-GCRMA/R/01b.downloadRawData.R
aroma.affymetrix/inst/vignettes/replication-GCRMA/doGCRMA_vs_gcrma.md.rsp
aroma.affymetrix/inst/vignettes/CRMA,Mapping50K_Hind240,BiasCorrectedChrXY.R
aroma.affymetrix/inst/vignettes/CRMAv2,Mapping50K_Hind240.R
aroma.affymetrix/inst/vignettes/replication-CRLMM
aroma.affymetrix/inst/vignettes/replication-CRLMM/R
aroma.affymetrix/inst/vignettes/replication-CRLMM/R/01a.downloadAnnotData.R
aroma.affymetrix/inst/vignettes/replication-CRLMM/R/01b.downloadRawData.R
aroma.affymetrix/inst/vignettes/replication-CRLMM/justSNPRMA_vs_oligo.md.rsp
aroma.affymetrix/inst/vignettes/replication-CRLMM/CRLMM_vs_oligo.md.rsp
aroma.affymetrix/inst/testScripts
aroma.affymetrix/inst/testScripts/setup
aroma.affymetrix/inst/testScripts/setup/01c.installAllPackages.R
aroma.affymetrix/inst/testScripts/setup/spawnTests.sh
aroma.affymetrix/inst/testScripts/setup/99a.cleanupRootDirectories.R
aroma.affymetrix/inst/testScripts/setup/01a.downloadAllAnnotationData.R
aroma.affymetrix/inst/testScripts/setup/01b.downloadAllRawDataSet.R
aroma.affymetrix/inst/testScripts/annotation
aroma.affymetrix/inst/testScripts/annotation/chipTypes
aroma.affymetrix/inst/testScripts/annotation/chipTypes/GenomeWideSNP_6
aroma.affymetrix/inst/testScripts/annotation/chipTypes/GenomeWideSNP_6/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/annotation/chipTypes/GenomeWideSNP_6/11.UFL.R
aroma.affymetrix/inst/testScripts/annotation/chipTypes/GenomeWideSNP_6/21.UGP.R
aroma.affymetrix/inst/testScripts/testAll.R
aroma.affymetrix/inst/testScripts/addons
aroma.affymetrix/inst/testScripts/addons/chipTypes
aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping50K_Hind240
aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping50K_Hind240/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping50K_Hind240/01c.installPackages.R
aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping50K_Hind240/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping50K_Hind240/21.doACNE,seg.R
aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp,Sty
aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp,Sty/11.doASCRMAv2,TCNs,500K.R
aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp,Sty/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp,Sty/01c.installPackages.R
aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp,Sty/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp
aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp/31.doASCRMAv2,PSCBS.R
aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp/21.doASCRMAv2,CalMaTe.R
aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp/01c.installPackages.R
aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/launch.R
aroma.affymetrix/inst/testScripts/R
aroma.affymetrix/inst/testScripts/R/installUtils.R
aroma.affymetrix/inst/testScripts/R/downloadUtils.R
aroma.affymetrix/inst/testScripts/R/launchUtils.R
aroma.affymetrix/inst/testScripts/replication
aroma.affymetrix/inst/testScripts/replication/chipTypes
aroma.affymetrix/inst/testScripts/replication/chipTypes/GenomeWideSNP_6
aroma.affymetrix/inst/testScripts/replication/chipTypes/GenomeWideSNP_6/11.justSNPRMA_vs_oligo.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/GenomeWideSNP_6/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/GenomeWideSNP_6/01c.installPackages.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/GenomeWideSNP_6/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2
aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/12.doGCRMA_vs_gcrma.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/11.doRMA_vs_affyPLM.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/01c.installPackages.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/11.doRMA_vs_oligo.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/21.justRMA_vs_affy.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping50K_Hind240
aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping50K_Hind240/01a.downloadAnnotData.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping50K_Hind240/11.justSNPRMA_vs_oligo.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping50K_Hind240/12.CRLMM_vs_oligo.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping50K_Hind240/01c.installPackages.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping50K_Hind240/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/Hs_PromPR_v02
aroma.affymetrix/inst/testScripts/replication/chipTypes/Hs_PromPR_v02/11.MatNormalization_vs_MAT.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/Hs_PromPR_v02/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/Hs_PromPR_v02/01c.installPackages.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/Hs_PromPR_v02/21.MatSmoothing_vs_MAT.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/Hs_PromPR_v02/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping250K_Nsp
aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping250K_Nsp/11.justSNPRMA_vs_oligo.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping250K_Nsp/12.CRLMM_vs_oligo.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping250K_Nsp/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping250K_Nsp/01c.installPackages.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping250K_Nsp/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/parallel
aroma.affymetrix/inst/testScripts/parallel/chipTypes
aroma.affymetrix/inst/testScripts/parallel/chipTypes/Mapping10K_Xba142
aroma.affymetrix/inst/testScripts/parallel/chipTypes/Mapping10K_Xba142/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/parallel/chipTypes/Mapping10K_Xba142/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/parallel/chipTypes/Mapping10K_Xba142/21a,doCBS.R
aroma.affymetrix/inst/testScripts/parallel/chipTypes/Mapping10K_Xba142/11a,doASCRMAv2.R
aroma.affymetrix/inst/testScripts/archive
aroma.affymetrix/inst/testScripts/archive/system
aroma.affymetrix/inst/testScripts/archive/system/chipTypes
aroma.affymetrix/inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty
aroma.affymetrix/inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/31.ASCN,paired.R
aroma.affymetrix/inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/31.ASCN.R
aroma.affymetrix/inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/21.TCN,500K.R
aroma.affymetrix/inst/testScripts/setup.R
aroma.affymetrix/inst/testScripts/futures
aroma.affymetrix/inst/testScripts/futures/GenomeWideSNP_6
aroma.affymetrix/inst/testScripts/futures/GenomeWideSNP_6/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/futures/GenomeWideSNP_6/11.BasePositionNormalization.R
aroma.affymetrix/inst/testScripts/futures/GenomeWideSNP_6/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/futures/GenomeWideSNP_6/11.AllelicCrosstalkCalibration.R
aroma.affymetrix/inst/testScripts/futures/HG-U133_Plus_2
aroma.affymetrix/inst/testScripts/futures/HG-U133_Plus_2/11.OpticalBackgroundCorrection.R
aroma.affymetrix/inst/testScripts/futures/HG-U133_Plus_2/12.GcRmaBackgroundCorrection.R
aroma.affymetrix/inst/testScripts/futures/HG-U133_Plus_2/13.RmaBackgroundCorrection.R
aroma.affymetrix/inst/testScripts/futures/HG-U133_Plus_2/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/futures/HG-U133_Plus_2/14.NormExpBackgroundCorrection.R
aroma.affymetrix/inst/testScripts/futures/HG-U133_Plus_2/01c.installPackages.R
aroma.affymetrix/inst/testScripts/futures/HG-U133_Plus_2/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/futures/Hs_PromPR_v02
aroma.affymetrix/inst/testScripts/futures/Hs_PromPR_v02/11.MatNormalization.R
aroma.affymetrix/inst/testScripts/futures/Hs_PromPR_v02/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/futures/Hs_PromPR_v02/01c.installPackages.R
aroma.affymetrix/inst/testScripts/futures/Hs_PromPR_v02/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/futures/Mapping10K_Xba142
aroma.affymetrix/inst/testScripts/futures/Mapping10K_Xba142/11.UniqueCDF.R
aroma.affymetrix/inst/testScripts/futures/Mapping10K_Xba142/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/futures/Mapping10K_Xba142/11.BasePositionNormalization.R
aroma.affymetrix/inst/testScripts/futures/Mapping10K_Xba142/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/futures/Mapping10K_Xba142/11.AllelicCrosstalkCalibration.R
aroma.affymetrix/inst/testScripts/system
aroma.affymetrix/inst/testScripts/system/chipTypes
aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6
aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,plots.R
aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,GCNorm.R
aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2.R
aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/11.justSNPRMA.R
aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/01c.installPackages.R
aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,ArrayExplorer.R
aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,extract.R
aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,AlleleSummation.R
aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,singleArray.R
aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,plotACC.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/41.BCN.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/11.RmaPlm.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/31.ASCRMA.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/42.BPN,AS.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/51.ACC,merge.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/01a.downloadAnnotData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/42.BPN.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/21.CRMA,QA.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/61.TCN,XYbias.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/21.CRMA.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/71.doCBS,tuple.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/21.CRMA,paired.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/81.fnt.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Test3
aroma.affymetrix/inst/testScripts/system/chipTypes/Test3/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Test3/11.ArrayExplorer.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Test3/01d.downloadRawData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Test3/01c.installPackages.R
aroma.affymetrix/inst/testScripts/system/chipTypes/HG-U133_Plus_2
aroma.affymetrix/inst/testScripts/system/chipTypes/HG-U133_Plus_2/11.doRMA,ArrayExplorer.R
aroma.affymetrix/inst/testScripts/system/chipTypes/HG-U133_Plus_2/11.doRMA.R
aroma.affymetrix/inst/testScripts/system/chipTypes/HG-U133_Plus_2/11.doRMA,PLM,withPriors.R
aroma.affymetrix/inst/testScripts/system/chipTypes/HG-U133_Plus_2/81.doRMA,extractExpressionSet.R
aroma.affymetrix/inst/testScripts/system/chipTypes/HG-U133_Plus_2/21.BackgroundCorrections.R
aroma.affymetrix/inst/testScripts/system/chipTypes/HG-U133_Plus_2/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/HG-U133_Plus_2/01c.installPackages.R
aroma.affymetrix/inst/testScripts/system/chipTypes/HG-U133_Plus_2/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/HG-U133_Plus_2/81.doRMA,extractAffyBatch.R
aroma.affymetrix/inst/testScripts/system/chipTypes/HG-U133_Plus_2/12.doGCRMA.R
aroma.affymetrix/inst/testScripts/system/chipTypes/CytoScanHD_Array
aroma.affymetrix/inst/testScripts/system/chipTypes/CytoScanHD_Array/21.doASCRMAv2,PSCN.R
aroma.affymetrix/inst/testScripts/system/chipTypes/CytoScanHD_Array/21,doASCRMAv2.R
aroma.affymetrix/inst/testScripts/system/chipTypes/CytoScanHD_Array/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/CytoScanHD_Array/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/CytoScanHD_Array/21,doASCRMAv2,CBS.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Sty
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Sty/22.doASCRMAv2,singleArray.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Sty/21.doASCRMAv2.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Sty/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Sty/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Sty/21.doASCRMAv2,ArrayExplorer.R
aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_5
aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_5/21.doASCRMAv2.R
aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_5/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_5/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_5/21.doASCRMAv2,ArrayExplorer.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240/21.doASCRMAv2.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240/11.justSNPRMA.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240/01c.installPackages.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240/21.doASCRMAv2,ArrayExplorer.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240/10.CDF,groupUnitsBy.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240/12.justSNPRMA,CRLMM.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240/21.doASCRMAv2,plotACC.R
aroma.affymetrix/inst/testScripts/system/chipTypes/MOUSEDIVm520650
aroma.affymetrix/inst/testScripts/system/chipTypes/MOUSEDIVm520650/21.doASCRMAv2.R
aroma.affymetrix/inst/testScripts/system/chipTypes/MOUSEDIVm520650/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/MOUSEDIVm520650/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Hs_PromPR_v02
aroma.affymetrix/inst/testScripts/system/chipTypes/Hs_PromPR_v02/11.MatNormalization.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Hs_PromPR_v02/21.MatSmoothing.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Hs_PromPR_v02/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Hs_PromPR_v02/01c.installPackages.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Hs_PromPR_v02/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Hs_PromPR_v02/31.AromaCellCpgFile.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mm_PromPR_v02
aroma.affymetrix/inst/testScripts/system/chipTypes/Mm_PromPR_v02/10,CDF,unique.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mm_PromPR_v02/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/MoEx-1_0-st-v1
aroma.affymetrix/inst/testScripts/system/chipTypes/MoEx-1_0-st-v1/11.GcRmaBackgroundCorrection.R
aroma.affymetrix/inst/testScripts/system/chipTypes/MoEx-1_0-st-v1/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/MoEx-1_0-st-v1/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/MoGene-1_0-st-v1
aroma.affymetrix/inst/testScripts/system/chipTypes/MoGene-1_0-st-v1/12.QuantileNormalization.R
aroma.affymetrix/inst/testScripts/system/chipTypes/MoGene-1_0-st-v1/11.RmaBackgroundCorrection.R
aroma.affymetrix/inst/testScripts/system/chipTypes/MoGene-1_0-st-v1/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/MoGene-1_0-st-v1/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2
aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/test20101202,gcrma.R
aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/21.doFIRMA,extras.R
aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/21.doFIRMA.R
aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/21.doFIRMA,QC.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,plotACC.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,plots,pairs.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/31.ACC,mergeShifts.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,singleArray.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,PSCN.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,FLN,zero.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,CBS.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/11.doCRMAv1.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,CBS,CE.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,HaarSeg.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/11.doCRMAv1,SmNorm.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,extractAndWrite.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,QA.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/01c.installPackages.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/31.doASCRMAv1.ArrayExplorer.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,extract.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,CBS,any.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/41.ACC,expectile.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/31.ACC,BCN.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,TotalFreqB.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,plots.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/12.doASCRMAv1.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,CBS,ref.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,GLAD.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/10.CDF,groupUnitsBy.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/10.CDF,readDataFrame.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Nsp
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Nsp/21.doASCRMAv1,ArrayExplorer.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Nsp/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Nsp/31.doASCRMAv2.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Nsp/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Nsp/31.doASCRMAv2,TumorNormalPair.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Cytogenetics_Array
aroma.affymetrix/inst/testScripts/system/chipTypes/Cytogenetics_Array/test20090828,cyto.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Cytogenetics_Array/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/system/chipTypes/Cytogenetics_Array/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/complete
aroma.affymetrix/inst/testScripts/complete/dataSets
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE27691
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE27691/21.doASCRMAv2.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE27691/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE27691/01c.installPackages.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE27691/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/22.doASCRMAv2,CalMaTe,Nsp.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/11.doASCRMAv2,Sty.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/31.doASCRMAv2,PairedPSCBS,Sty.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/32.doASCRMAv2,CalMaTe,PairedPSCBS,Sty.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/31.doASCRMAv2,PairedPSCBS,Nsp.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/32.doASCRMAv2,CalMaTe,PairedPSCBS,Nsp.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/11.doASCRMAv2,Nsp.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/01c.installPackages.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/22.doASCRMAv2,CalMaTe,Sty.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/GSE12702,samples.txt
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE13372
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE13372/GSE13372,samples.txt
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE13372/22.doASCRMAv2,CalMaTe.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE13372/31.doASCRMAv2,PairedPSCBS.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE13372/32.doASCRMAv2,CalMaTe,PairedPSCBS.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE13372/21.doASCRMAv2.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE13372/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE13372/01c.installPackages.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE13372/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE19539
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE19539/22.doASCRMAv2,CalMaTe.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE19539/21.doASCRMAv2.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE19539/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE19539/01c.installPackages.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE19539/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE20584
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE20584/GSE20584,samples.txt
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE20584/31.doASCRMAv2,PairedPSCBS.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE20584/21.doASCRMAv2.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE20584/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE20584/01c.installPackages.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE20584/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE34754
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE34754/GSE34754,samples.txt
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE34754/22.doASCRMAv2,CalMaTe.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE34754/31.doASCRMAv2,PairedPSCBS.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE34754/32.doASCRMAv2,CalMaTe,PairedPSCBS.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE34754/21.doASCRMAv2.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE34754/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE34754/01c.installPackages.R
aroma.affymetrix/inst/testScripts/complete/dataSets/GSE34754/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/robustness
aroma.affymetrix/inst/testScripts/robustness/chipTypes
aroma.affymetrix/inst/testScripts/robustness/chipTypes/Mapping50K_Hind240
aroma.affymetrix/inst/testScripts/robustness/chipTypes/Mapping50K_Hind240/01a.downloadAnnotData.R
aroma.affymetrix/inst/testScripts/robustness/chipTypes/Mapping50K_Hind240/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/robustness/chipTypes/Mapping50K_Hind240/21.doASCRMAv2,CRLMM.R
aroma.affymetrix/inst/testScripts/robustness/chipTypes/MoGene-1_0-st-v1
aroma.affymetrix/inst/testScripts/robustness/chipTypes/MoGene-1_0-st-v1/11.GcRmaBgCorr.R
aroma.affymetrix/inst/testScripts/robustness/chipTypes/MoGene-1_0-st-v1/01a.downloadAnnotationData.R
aroma.affymetrix/inst/testScripts/robustness/chipTypes/MoGene-1_0-st-v1/01b.downloadRawData.R
aroma.affymetrix/inst/testScripts/robustness/chipTypes/Mapping10K_Xba142
aroma.affymetrix/inst/testScripts/robustness/chipTypes/Mapping10K_Xba142/01a.downloadAnnotData.R
aroma.affymetrix/inst/testScripts/robustness/chipTypes/Mapping10K_Xba142/11.doASCRMAv1,CBS,invalid.R
aroma.affymetrix/inst/testScripts/robustness/chipTypes/Mapping10K_Xba142/01b.downloadRawData.R
aroma.affymetrix/inst/downloadScripts
aroma.affymetrix/inst/downloadScripts/chipTypes
aroma.affymetrix/inst/downloadScripts/chipTypes/Mapping50K_Hind240,Xba240
aroma.affymetrix/inst/downloadScripts/chipTypes/Mapping50K_Hind240,Xba240/HapMap,testSet,100K.R
aroma.affymetrix/inst/buildScripts
aroma.affymetrix/inst/buildScripts/chipTypes
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na31
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na31/GenomeWideSNP_6,UGP.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na31/GenomeWideSNP_6,default,UGP+UFL.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na31/GenomeWideSNP_6,UFL.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,UGP.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na32
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na32/GenomeWideSNP_6,UGP.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na32/GenomeWideSNP_6,default,UGP+UFL.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na32/GenomeWideSNP_6,UFL.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na33
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na33/GenomeWideSNP_6,UGP.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na33/GenomeWideSNP_6,default,UGP+UFL.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na33/GenomeWideSNP_6,UFL.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,default,UGP+UFL.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,UFL.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na26
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na26/GenomeWideSNP_6,UFL,na26.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na26/GenomeWideSNP_6,UGP,na26.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na26/GWS6,default,UGP+UFL,na26.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na27.1
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na27.1/GenomeWideSNP_6,UGP,na27.1.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na27.1/GenomeWideSNP_6,UFL,na27.1.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na27.1/GWS6,default,UGP+UFL,na27.1.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na25
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na25/GenomeWideSNP_6,UFL,na25.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na27
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na27/GenomeWideSNP_6,UGC,na27.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na30
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na30/GenomeWideSNP_6,UGP,na30.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na30/GenomeWideSNP_6,UFL,na30.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Xba240
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Xba240/Mapping50K_Xba240,ACS.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Xba240/Mapping50K_Xba240,UFL.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Xba240/Mapping50K_Xba240,UGP.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Xba240/na26
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Xba240/na26/Mapping50K_Xba240,UGP,na26.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Xba240/na26/Mapping50K_Xba240,UFL,na26.R
aroma.affymetrix/inst/buildScripts/chipTypes/HG-Focus
aroma.affymetrix/inst/buildScripts/chipTypes/HG-Focus/HG-Focus,ACS.R
aroma.affymetrix/inst/buildScripts/chipTypes/HG-U133A
aroma.affymetrix/inst/buildScripts/chipTypes/HG-U133A/HG-U133A,ACS.R
aroma.affymetrix/inst/buildScripts/chipTypes/CytoScanHD_Array
aroma.affymetrix/inst/buildScripts/chipTypes/CytoScanHD_Array/na32
aroma.affymetrix/inst/buildScripts/chipTypes/CytoScanHD_Array/na32/CytoScanHD_Array,UGP.R
aroma.affymetrix/inst/buildScripts/chipTypes/CytoScanHD_Array/na32/CytoScanHD_Array,UFL.R
aroma.affymetrix/inst/buildScripts/chipTypes/CytoScanHD_Array/CytoScanHD_Array,ACS.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Sty
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Sty/na31
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Sty/na31/Mapping250K_Sty,UGP,na31.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Sty/na31/Mapping250K_Sty,UFL,na31.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Sty/na28
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Sty/na28/Mapping250K_Sty,UGC,na28.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Sty/na26
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Sty/na26/Mapping250K_Sty,UFL,na26.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Sty/na26/Mapping250K_Sty,UGP,na26.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_5
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_5/na26
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GWS5,default,UGP+UFL,na26.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GenomeWideSNP_5,UFL,na26.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GenomeWideSNP_5,UFL,na26,GWS6.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GenomeWideSNP_5,UGP,na26.R
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_5/na25
aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_5/na25/GenomeWideSNP_5,UFL,na25,GWS6.R
aroma.affymetrix/inst/buildScripts/chipTypes/Canine_2
aroma.affymetrix/inst/buildScripts/chipTypes/Canine_2/Canine_2,ACS.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Hind240
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Hind240/Mapping50K_Hind240,UFL.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Hind240/Mapping50K_Xba240,UGP.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Hind240/na26
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Hind240/na26/Mapping50K_Hind240,UFL,na26.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Hind240/na26/Mapping50K_Hind240,UGP,na26.R
aroma.affymetrix/inst/buildScripts/chipTypes/MOUSEDIVm520650
aroma.affymetrix/inst/buildScripts/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650,ACS.R
aroma.affymetrix/inst/buildScripts/chipTypes/MOUSEDIVm520650/na30
aroma.affymetrix/inst/buildScripts/chipTypes/MOUSEDIVm520650/na30/MOUSEDIVm520650,UGP,na30.R
aroma.affymetrix/inst/buildScripts/chipTypes/MOUSEDIVm520650/na30/MOUSEDIVm520650,UFL,na30.R
aroma.affymetrix/inst/buildScripts/chipTypes/DogSty06m520431
aroma.affymetrix/inst/buildScripts/chipTypes/DogSty06m520431/DogSty06m520431,ACS.R
aroma.affymetrix/inst/buildScripts/chipTypes/HuGene-1_0-st-v1
aroma.affymetrix/inst/buildScripts/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,NetAffx.R
aroma.affymetrix/inst/buildScripts/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,ACS.R
aroma.affymetrix/inst/buildScripts/chipTypes/MoGene-1_0-st-v1
aroma.affymetrix/inst/buildScripts/chipTypes/MoGene-1_0-st-v1/MoGene-1_0-st-v1,ACS.R
aroma.affymetrix/inst/buildScripts/chipTypes/MoGene-1_0-st-v1/MoGene-1_0-st-v1,ACP.R
aroma.affymetrix/inst/buildScripts/chipTypes/MoGene-1_0-st-v1/MoGene-1_0-st-v1,UGP.R
aroma.affymetrix/inst/buildScripts/chipTypes/HuEx-1_0-st-v2
aroma.affymetrix/inst/buildScripts/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2,CDF,exonByTranscript.R
aroma.affymetrix/inst/buildScripts/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2,ACS.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping10K_Xba142
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping10K_Xba142/Mapping10K_Xba142,ACS.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping10K_Xba142/na26
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping10K_Xba142/na26/Mapping10K_Xba142,UFL,na26.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping10K_Xba142/na26/Mapping10K_Xba142,UGP,na26.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Nsp
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Nsp/na31
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Nsp/na31/Mapping250K_Nsp,UFL,na31.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Nsp/na31/Mapping250K_Nsp,UGP,na31.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Nsp/na28
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Nsp/na28/Mapping250K_Nsp,UGC,na28.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Nsp/na26
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Nsp/na26/Mapping250K_Nsp,UFL,na26.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Nsp/na26/Mapping250K_Nsp,UGP,na26.R
aroma.affymetrix/inst/buildScripts/chipTypes/Cytogenetics_Array
aroma.affymetrix/inst/buildScripts/chipTypes/Cytogenetics_Array/na28
aroma.affymetrix/inst/buildScripts/chipTypes/Cytogenetics_Array/na28/Cytogenetics_Array,UGP,na28.R
aroma.affymetrix/inst/buildScripts/chipTypes/Cytogenetics_Array/Cytogenetics_Array,ACS.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping10K_Xba131
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping10K_Xba131/na26
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping10K_Xba131/na26/Mapping10K_Xba131,UFL,na26.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping10K_Xba131/na26/Mapping10K_Xba131,UGP,na26.R
aroma.affymetrix/inst/buildScripts/chipTypes/Mapping10K_Xba131/Mapping10K_Xba131,ACS.R
aroma.affymetrix/tests
aroma.affymetrix/tests/AffymetrixCdfFile.R
aroma.affymetrix/tests/AffymetrixCelSet.R
aroma.affymetrix/tests/AffymetrixCelFile.R
aroma.affymetrix/tests/002.setupExampleData,rawData.R
aroma.affymetrix/tests/001.setupExampleData,annotationData.R
aroma.affymetrix/NAMESPACE
aroma.affymetrix/NEWS
aroma.affymetrix/R
aroma.affymetrix/R/ProbeLevelTransform.R
aroma.affymetrix/R/QualityAssessmentFile.R
aroma.affymetrix/R/BackgroundCorrection.R
aroma.affymetrix/R/ProbeLevelModel.calculateResiduals.R
aroma.affymetrix/R/LimmaBackgroundCorrection.R
aroma.affymetrix/R/SnpProbeAffinityFile.R
aroma.affymetrix/R/ResidualFile.R
aroma.affymetrix/R/SnpChipEffectFile.R
aroma.affymetrix/R/DChipCdfBinFile.R
aroma.affymetrix/R/CnChipEffectSet.importFromDChip.R
aroma.affymetrix/R/AffinePlm.R
aroma.affymetrix/R/GenomeInformation.AFFX.R
aroma.affymetrix/R/SingleArrayUnitModel.R
aroma.affymetrix/R/SnpPlm.R
aroma.affymetrix/R/ReseqCrosstalkCalibration.R
aroma.affymetrix/R/AffymetrixFileSetReporter.R
aroma.affymetrix/R/AffymetrixCelFile.extractMatrix.R
aroma.affymetrix/R/AffymetrixCelFile.BG.R
aroma.affymetrix/R/ProbeLevelModel.fit.R
aroma.affymetrix/R/AffymetrixCdfFile.MONOCELL.R
aroma.affymetrix/R/isUnitGroupCellMap.R
aroma.affymetrix/R/DChipDcpFile.R
aroma.affymetrix/R/AffymetrixPlatform.R
aroma.affymetrix/R/ParameterCelSet.R
aroma.affymetrix/R/AffymetrixCelSet.BG.R
aroma.affymetrix/R/CnagCfhFile.R
aroma.affymetrix/R/AffymetrixProbeTabFile.R
aroma.affymetrix/R/ChipEffectSet.PLOT.R
aroma.affymetrix/R/CnChipEffectFile.R
aroma.affymetrix/R/ChipEffectGroupMerge.R
aroma.affymetrix/R/021.dynamic_imports.R
aroma.affymetrix/R/GenomeInformation.R
aroma.affymetrix/R/QualityAssessmentSet.R
aroma.affymetrix/R/AromaCellMatchScoreFile.R
aroma.affymetrix/R/000.R
aroma.affymetrix/R/SnpCnvQSet.extractTheta.R
aroma.affymetrix/R/AffymetrixCdfFile.readDataFrame.R
aroma.affymetrix/R/AllelicCrosstalkCalibration.getSetsOfProbes.R
aroma.affymetrix/R/createExonByTranscriptCdf.R
aroma.affymetrix/R/ChipEffectSetTuple.R
aroma.affymetrix/R/UnitModel.R
aroma.affymetrix/R/AffymetrixCelSetReporter.R
aroma.affymetrix/R/AllelicCrosstalkCalibration.R
aroma.affymetrix/R/WeightsFile.R
aroma.affymetrix/R/AbstractProbeSequenceNormalization.R
aroma.affymetrix/R/AffymetrixCelSet.extractMatrix.R
aroma.affymetrix/R/AromaUnitTabularBinaryFile.AFFX.PLOT.R
aroma.affymetrix/R/SingleArrayUnitModel.fit.R
aroma.affymetrix/R/UflSnpInformation.R
aroma.affymetrix/R/SmoothMultiarrayModel.R
aroma.affymetrix/R/ChipEffectSet.getBaseline.R
aroma.affymetrix/R/FirmaSet.R
aroma.affymetrix/R/AffymetrixCsvFile.R
aroma.affymetrix/R/doCRMAv1.R
aroma.affymetrix/R/AffymetrixCdfFile.R
aroma.affymetrix/R/AromaUfcFile.R
aroma.affymetrix/R/QuantileNormalization.xtra.R
aroma.affymetrix/R/AffymetrixCdfFile.SNPs.R
aroma.affymetrix/R/AromaCellPositionFile.AFFX.R
aroma.affymetrix/R/AllelicCrosstalkCalibration.PLOT.R
aroma.affymetrix/R/ChipEffectFile.fromDataFile.R
aroma.affymetrix/R/AffymetrixAptSummaryFile.R
aroma.affymetrix/R/AromaUnitTabularBinaryFile.AFFX.R
aroma.affymetrix/R/AffymetrixCelSet.R
aroma.affymetrix/R/AffymetrixCelFile.PLOT.R
aroma.affymetrix/R/ASCRMAv2.R
aroma.affymetrix/R/HetLogAddCnPlm.R
aroma.affymetrix/R/ProbeLevelTransform3.R
aroma.affymetrix/R/AromaUnitGcContentFile.AFFX.R
aroma.affymetrix/R/AffymetrixCdfFile.getAlleleCellPairs.R
aroma.affymetrix/R/profileCGH.getRegions.R
aroma.affymetrix/R/readCdfGroupStrands.R
aroma.affymetrix/R/SnpQSet.extractTheta.R
aroma.affymetrix/R/DChipCdfBinFile.mapToUnitNamesFile.R
aroma.affymetrix/R/SmoothSaModel.R
aroma.affymetrix/R/AromaPipeline.R
aroma.affymetrix/R/AffymetrixNetAffxCsvFile.XTRS.R
aroma.affymetrix/R/OpticalBackgroundCorrection.R
aroma.affymetrix/R/ChipEffectSet.calculateBaseline.R
aroma.affymetrix/R/999.DEPRECATED.R
aroma.affymetrix/R/bpmapCluster2Cdf.R
aroma.affymetrix/R/MatNormalization.R
aroma.affymetrix/R/AffymetrixCdfFile.COUNTS.R
aroma.affymetrix/R/ExonProbeAffinityFile.R
aroma.affymetrix/R/CnChipEffectSet.importFromApt.R
aroma.affymetrix/R/AffymetrixCelSetTuple.R
aroma.affymetrix/R/009.setup.R
aroma.affymetrix/R/GenericReporter.R
aroma.affymetrix/R/Model.R
aroma.affymetrix/R/AffymetrixCelSet.getAverageFile.R
aroma.affymetrix/R/findByCdf2.R
aroma.affymetrix/R/ChipEffectFile.R
aroma.affymetrix/R/CrlmmParametersFile.R
aroma.affymetrix/R/MbeiSnpPlm.R
aroma.affymetrix/R/AffymetrixCelFile.normalizeAffine.R
aroma.affymetrix/R/SnpChipEffectSet.extractTotalAndFreqB.R
aroma.affymetrix/R/CnChipEffectSetTuple.R
aroma.affymetrix/R/profileCGH.writeRegions.R
aroma.affymetrix/R/ChipEffectSet.TOFULL.R
aroma.affymetrix/R/DChipDcpSet.extras.R
aroma.affymetrix/R/plotBoxplotStats.list.R
aroma.affymetrix/R/TransformReport.R
aroma.affymetrix/R/CnChipEffectSet.R
aroma.affymetrix/R/UnitModel.fitCnProbes.R
aroma.affymetrix/R/AvgCnPlm.R
aroma.affymetrix/R/randomSeed.R
aroma.affymetrix/R/AdditiveCovariatesNormalization.R
aroma.affymetrix/R/AvgSnpPlm.R
aroma.affymetrix/R/ScaleNormalization3.R
aroma.affymetrix/R/AffymetrixCdfFile.getProbeSequenceData.R
aroma.affymetrix/R/AffymetrixCnChpSet.R
aroma.affymetrix/R/ChipEffectSet.extractExpressionSet.R
aroma.affymetrix/R/ExonRmaPlm.R
aroma.affymetrix/R/readCfnHeader.R
aroma.affymetrix/R/DChipDcpSet.R
aroma.affymetrix/R/AffymetrixCelSet.extractFeatureSet.R
aroma.affymetrix/R/fitPlasqUnit.R
aroma.affymetrix/R/setupExampleData.R
aroma.affymetrix/R/SpatialReporter.R
aroma.affymetrix/R/AffymetrixCdfFile.UNIQUE.R
aroma.affymetrix/R/WeightsSet.R
aroma.affymetrix/R/SnpChipEffectNnn.writeCNT.R
aroma.affymetrix/R/CnagCfhSet.R
aroma.affymetrix/R/SmoothRmaModel.R
aroma.affymetrix/R/AffymetrixCelFile.normalizeQuantile.R
aroma.affymetrix/R/MbeiCnPlm.R
aroma.affymetrix/R/MultiArrayUnitModel.R
aroma.affymetrix/R/AffymetrixCelFile.R
aroma.affymetrix/R/AffymetrixCelSet.extractAffyBatch.R
aroma.affymetrix/R/AffymetrixCelSet.justSNPRMA.R
aroma.affymetrix/R/MatSmoothing.R
aroma.affymetrix/R/readCfnUnits.R
aroma.affymetrix/R/QuantileNormalization.R
aroma.affymetrix/R/CnPlm.R
aroma.affymetrix/R/ChipEffectFile.getUnitGroupCellMatrixMap.R
aroma.affymetrix/R/HetLogAddPlm.R
aroma.affymetrix/R/AffymetrixCelSet.importFromDChip.R
aroma.affymetrix/R/doCRMAv2.R
aroma.affymetrix/R/AffymetrixCelFile.fitQuantileNormFcn.R
aroma.affymetrix/R/doFIRMA.R
aroma.affymetrix/R/RmaPlm.R
aroma.affymetrix/R/AromaUgpFile.AFFX.R
aroma.affymetrix/R/Package.XTRA.R
aroma.affymetrix/R/pdInfo2Cdf.R
aroma.affymetrix/R/SnpChipEffectSet.R
aroma.affymetrix/R/SnpChipEffectSet.extractSnpQSet.R
aroma.affymetrix/R/CrlmmParametersSet.R
aroma.affymetrix/R/AffymetrixCdfFile.getAlleleProbePairs3.R
aroma.affymetrix/R/AffyGenePDInfo.writeCdf.R
aroma.affymetrix/R/AromaCellCpgFile.AFFX.R
aroma.affymetrix/R/justRMA.R
aroma.affymetrix/R/ExonChipEffectSet.R
aroma.affymetrix/R/GcContentNormalization2.plotCovariateEffects.R
aroma.affymetrix/R/ChromosomalModel.AFFX.R
aroma.affymetrix/R/ResidualSet.R
aroma.affymetrix/R/ChipEffectSet.R
aroma.affymetrix/R/SmoothMultiarrayModel.fit.R
aroma.affymetrix/R/CopyNumberChromosomalModel.applyCCF.R
aroma.affymetrix/R/ChipEffectFile.xam.R
aroma.affymetrix/R/CrlmmModel.EXT.R
aroma.affymetrix/R/env2Cdf.R
aroma.affymetrix/R/ExonRmaPlm.calculateWeights.R
aroma.affymetrix/R/AffymetrixCelSet.writeSgr.R
aroma.affymetrix/R/FragmentEquivalentClassNormalization.R
aroma.affymetrix/R/AffymetrixCdfFile.getCellQuartets.R
aroma.affymetrix/R/MbeiPlm.R
aroma.affymetrix/R/AffymetrixCdfFile.getUnitGroupNamesFromUgcMap.R
aroma.affymetrix/R/AffineCnPlm.R
aroma.affymetrix/R/readCfhUnits.R
aroma.affymetrix/R/AffymetrixCdfFile.getSubsetOfCellIndices.R
aroma.affymetrix/R/AromaCellMatchScoreFile.AFFX.R
aroma.affymetrix/R/GcContentNormalization2.R
aroma.affymetrix/R/AffymetrixCelSet.PLOT.R
aroma.affymetrix/R/AffymetrixFileSet.getIdentifier.R
aroma.affymetrix/R/SnpChipEffectFile.extractTotalAndFracB.R
aroma.affymetrix/R/AffymetrixTabularFile.R
aroma.affymetrix/R/dropCellsFromCdfList.R
aroma.affymetrix/R/UgpGenomeInformation.R
aroma.affymetrix/R/SnpChipEffectSet.extractAlleleSet.R
aroma.affymetrix/R/CnProbeAffinityFile.R
aroma.affymetrix/R/SpatialRowColumnNormalization.R
aroma.affymetrix/R/SnpChipEffectSet.extractSnpCnvQSet.R
aroma.affymetrix/R/QualityAssessmentModel.R
aroma.affymetrix/R/DChipGenomeInformation.R
aroma.affymetrix/R/AffymetrixCdfFile.PLOT.R
aroma.affymetrix/R/ArrayExplorer.R
aroma.affymetrix/R/readCfhHeader.R
aroma.affymetrix/R/ChipEffectSet.extractTheta.R
aroma.affymetrix/R/FirmaModel.R
aroma.affymetrix/R/AvgPlm.R
aroma.affymetrix/R/SnpInformation.R
aroma.affymetrix/R/LinearModelProbeSequenceNormalization.R
aroma.affymetrix/R/Transform.R
aroma.affymetrix/R/ParameterCelFile.R
aroma.affymetrix/R/doGCRMA.R
aroma.affymetrix/R/AffymetrixCdfFile.getAlleleProbePairs2.R
aroma.affymetrix/R/AffymetrixCdfFile.writeCdfByExcludingCells.R
aroma.affymetrix/R/006.fixVarArgs.R
aroma.affymetrix/R/ChipEffectTransform.R
aroma.affymetrix/R/ProbeLevelModel.calculateWeights.R
aroma.affymetrix/R/AffymetrixPgfFile.R
aroma.affymetrix/R/DChipSnpInformation.R
aroma.affymetrix/R/AffymetrixTsvFile.R
aroma.affymetrix/R/DChipQuantileNormalization.R
aroma.affymetrix/R/CopyNumberSegmentationModel.migrateTool.R
aroma.affymetrix/R/ProbeAffinityFile.R
aroma.affymetrix/R/UnitTypeScaleNormalization.R
aroma.affymetrix/R/ParameterCelFile.extractNnn.R
aroma.affymetrix/R/ExonChipEffectFile.R
aroma.affymetrix/R/doRMA.R
aroma.affymetrix/R/NormExpBackgroundCorrection.R
aroma.affymetrix/R/AffineSnpPlm.R
aroma.affymetrix/R/ChipEffectFile.extractTheta.R
aroma.affymetrix/R/AlleleSummation.R
aroma.affymetrix/R/SnpChipEffectSet.exportTotalAndFracB.R
aroma.affymetrix/R/AffymetrixFileSet.R
aroma.affymetrix/R/999.AromaAffymetrix.R
aroma.affymetrix/R/FragmentLengthNormalization.R
aroma.affymetrix/R/ChipEffectNnn.extractChromosomalDataFrame.R
aroma.affymetrix/R/ChipEffectSet.STATS.R
aroma.affymetrix/R/AffymetrixCdfFile.getAlleleProbePairs.R
aroma.affymetrix/R/AffymetrixCelFile.createFrom.R
aroma.affymetrix/R/AffymetrixCdfFile.getSubsetOfUnits.R
aroma.affymetrix/R/AffymetrixCnChpFile.R
aroma.affymetrix/R/SnpChipEffectFile.exportTotalAndFracB.R
aroma.affymetrix/R/CnChipEffectSet.writeWig.R
aroma.affymetrix/R/BaseCountNormalization.R
aroma.affymetrix/R/CrlmmModel.R
aroma.affymetrix/R/RmaCnPlm.R
aroma.affymetrix/R/AromaCellMatchScoreFile.importFromBpmap.R
aroma.affymetrix/R/BasePositionNormalization.R
aroma.affymetrix/R/getPlasqTypes.R
aroma.affymetrix/R/AffymetrixCelSet.NORM.R
aroma.affymetrix/R/AffymetrixCdfFile.getUnitGroupCellMap.R
aroma.affymetrix/R/AffymetrixCdfFile.groupUnitsByDimension.R
aroma.affymetrix/R/999.NonDocumentedObjects.R
aroma.affymetrix/R/999.package.R
aroma.affymetrix/R/ChromosomalModel.getPositionChipTypeUnit.R
aroma.affymetrix/R/CnChipEffectFile.exportAromaSignalBinaryFileList.R
aroma.affymetrix/R/BasePositionNormalization.getFit.R
aroma.affymetrix/R/SnpChipEffectGroupMerge.R
aroma.affymetrix/R/AffymetrixCdfFile.computeAffinities.R
aroma.affymetrix/R/HetLogAddSnpPlm.R
aroma.affymetrix/R/setCustomFindCdf.R
aroma.affymetrix/R/AffymetrixCelSet.convertToUnique.R
aroma.affymetrix/R/AffymetrixCsvGenomeInformation.R
aroma.affymetrix/R/ProbeLevelModel.R
aroma.affymetrix/R/AffymetrixFile.R
aroma.affymetrix/R/ChipEffectSet.xam.R
aroma.affymetrix/R/zzz.R
aroma.affymetrix/R/RmaBackgroundCorrection.R
aroma.affymetrix/R/SnpChipEffectNnn.extractCNT.R
aroma.affymetrix/R/AromaCellSequenceFile.importFromBpmap.R
aroma.affymetrix/R/AffymetrixCelFile.allocateFromCdf.R
aroma.affymetrix/R/AromaChipTypeAnnotationFile.R
aroma.affymetrix/R/GcContentNormalization.R
aroma.affymetrix/R/GcRmaBackgroundCorrection.R
aroma.affymetrix/R/AffymetrixNetAffxCsvFile.R
aroma.affymetrix/R/ScaleNormalization.R
aroma.affymetrix/R/FirmaFile.R
aroma.affymetrix/R/AromaCellSequenceFile.AFFX.R
aroma.affymetrix/R/AffymetrixCnChpSet.extras.R
aroma.affymetrix/R/AromaUflFile.AFFX.R
aroma.affymetrix/R/RmaSnpPlm.R
aroma.affymetrix/R/ChipEffectFile.TOFULL.R
aroma.affymetrix/R/ChromosomalModel.getXTheta.R
aroma.affymetrix/MD5
aroma.affymetrix/DESCRIPTION
aroma.affymetrix/man
aroma.affymetrix/man/getCellIndices.AffymetrixCdfFile.Rd
aroma.affymetrix/man/clearData.AffymetrixCelFile.Rd
aroma.affymetrix/man/DChipCdfBinFile.Rd
aroma.affymetrix/man/getAM.ChipEffectSet.Rd
aroma.affymetrix/man/AffineCnPlm.Rd
aroma.affymetrix/man/getImage.AffymetrixCelFile.Rd
aroma.affymetrix/man/randomSeed.Rd
aroma.affymetrix/man/WeightsSet.Rd
aroma.affymetrix/man/ProbeLevelTransform3.Rd
aroma.affymetrix/man/getCdf.CnagCfhSet.Rd
aroma.affymetrix/man/getCellIndices.CnChipEffectFile.Rd
aroma.affymetrix/man/extractMatrix.AffymetrixCelSet.Rd
aroma.affymetrix/man/fromFile.AffymetrixPgfFile.Rd
aroma.affymetrix/man/process.AllelicCrosstalkCalibration.Rd
aroma.affymetrix/man/getCellIndices.FirmaFile.Rd
aroma.affymetrix/man/setupExampleData.AromaAffymetrix.Rd
aroma.affymetrix/man/readUnits.MultiArrayUnitModel.Rd
aroma.affymetrix/man/setArrays.ArrayExplorer.Rd
aroma.affymetrix/man/process.ChipEffectGroupMerge.Rd
aroma.affymetrix/man/DChipQuantileNormalization.Rd
aroma.affymetrix/man/justRMA.Rd
aroma.affymetrix/man/fit.ProbeLevelModel.Rd
aroma.affymetrix/man/CnagCfhFile.Rd
aroma.affymetrix/man/verify.GenomeInformation.Rd
aroma.affymetrix/man/byChipType.GenomeInformation.Rd
aroma.affymetrix/man/byPath.AffymetrixFileSet.Rd
aroma.affymetrix/man/ReseqCrosstalkCalibration.Rd
aroma.affymetrix/man/SnpProbeAffinityFile.Rd
aroma.affymetrix/man/convert.AffymetrixCdfFile.Rd
aroma.affymetrix/man/AffymetrixCdfFile.Rd
aroma.affymetrix/man/process.GenericReporter.Rd
aroma.affymetrix/man/getCdf.CnagCfhFile.Rd
aroma.affymetrix/man/HetLogAddPlm.Rd
aroma.affymetrix/man/findUnitsTodo.UnitModel.Rd
aroma.affymetrix/man/CnProbeAffinityFile.Rd
aroma.affymetrix/man/ChipEffectTransform.Rd
aroma.affymetrix/man/GenericReporter.Rd
aroma.affymetrix/man/BaseCountNormalization.Rd
aroma.affymetrix/man/MbeiSnpPlm.Rd
aroma.affymetrix/man/getName.TransformReport.Rd
aroma.affymetrix/man/fromFile.AromaChipTypeAnnotationFile.Rd
aroma.affymetrix/man/process.AdditiveCovariatesNormalization.Rd
aroma.affymetrix/man/Model.Rd
aroma.affymetrix/man/getData.GenomeInformation.Rd
aroma.affymetrix/man/AvgSnpPlm.Rd
aroma.affymetrix/man/getInputDataSet.TransformReport.Rd
aroma.affymetrix/man/getFirmaSet.FirmaModel.Rd
aroma.affymetrix/man/getHeader.AffymetrixCdfFile.Rd
aroma.affymetrix/man/pdInfo2Cdf.Rd
aroma.affymetrix/man/SnpChipEffectSet.Rd
aroma.affymetrix/man/ExonProbeAffinityFile.Rd
aroma.affymetrix/man/CrlmmParametersSet.Rd
aroma.affymetrix/man/extractExpressionSet.ChipEffectSet.Rd
aroma.affymetrix/man/extractFeatureSet.AffymetrixCelSet.Rd
aroma.affymetrix/man/importFromApt.CnChipEffectSet.Rd
aroma.affymetrix/man/RmaSnpPlm.Rd
aroma.affymetrix/man/getPositions.GenomeInformation.Rd
aroma.affymetrix/man/getFitUnitGroupFunction.HetLogAddPlm.Rd
aroma.affymetrix/man/SnpChipEffectFile.Rd
aroma.affymetrix/man/RmaCnPlm.Rd
aroma.affymetrix/man/isSnpChip.AffymetrixCdfFile.Rd
aroma.affymetrix/man/getPath.Model.Rd
aroma.affymetrix/man/getRootPath.Model.Rd
aroma.affymetrix/man/readUnits.AffymetrixCdfFile.Rd
aroma.affymetrix/man/AffymetrixPgfFile.Rd
aroma.affymetrix/man/DChipDcpFile.Rd
aroma.affymetrix/man/setCdf.CnagCfhFile.Rd
aroma.affymetrix/man/importFromDChip.AffymetrixCelSet.Rd
aroma.affymetrix/man/as.CnagCfhSet.CnagCfhSet.Rd
aroma.affymetrix/man/nbrOfSnps.AffymetrixCdfFile.Rd
aroma.affymetrix/man/getCellIndices.SnpChipEffectFile.Rd
aroma.affymetrix/man/process.GcRmaBackgroundCorrection.Rd
aroma.affymetrix/man/doFIRMA.Rd
aroma.affymetrix/man/extractMatrix.ParameterCelSet.Rd
aroma.affymetrix/man/getOutputDataSet.Transform.Rd
aroma.affymetrix/man/AromaChipTypeAnnotationFile.Rd
aroma.affymetrix/man/fit.Model.Rd
aroma.affymetrix/man/setupExampleData.Rd
aroma.affymetrix/man/CnagCfhSet.Rd
aroma.affymetrix/man/getFitUnitGroupFunction.AffinePlm.Rd
aroma.affymetrix/man/process.ScaleNormalization.Rd
aroma.affymetrix/man/byChipType.DChipGenomeInformation.Rd
aroma.affymetrix/man/ResidualFile.Rd
aroma.affymetrix/man/AffymetrixFileSetReporter.Rd
aroma.affymetrix/man/HetLogAddCnPlm.Rd
aroma.affymetrix/man/process.FragmentLengthNormalization.Rd
aroma.affymetrix/man/SnpChipEffectGroupMerge.Rd
aroma.affymetrix/man/as.character.AffymetrixCelSet.Rd
aroma.affymetrix/man/GcRmaBackgroundCorrection.Rd
aroma.affymetrix/man/fit.FirmaModel.Rd
aroma.affymetrix/man/as.AffymetrixCelSet.AffymetrixCelSet.Rd
aroma.affymetrix/man/averageQuantile.AffymetrixCelSet.Rd
aroma.affymetrix/man/process.GcContentNormalization.Rd
aroma.affymetrix/man/getHeader.AromaChipTypeAnnotationFile.Rd
aroma.affymetrix/man/as.AffymetrixCnChpSet.AffymetrixCnChpSet.Rd
aroma.affymetrix/man/getAlleleCellPairs.AffymetrixCdfFile.Rd
aroma.affymetrix/man/getChipType.AffymetrixCelFile.Rd
aroma.affymetrix/man/TransformReport.Rd
aroma.affymetrix/man/process.MatNormalization.Rd
aroma.affymetrix/man/getHeader.AffymetrixPgfFile.Rd
aroma.affymetrix/man/getSnpNames.AffymetrixCdfFile.Rd
aroma.affymetrix/man/fit.SingleArrayUnitModel.Rd
aroma.affymetrix/man/process.OpticalBackgroundCorrection.Rd
aroma.affymetrix/man/computeAffinities.AffymetrixCdfFile.Rd
aroma.affymetrix/man/isPm.AffymetrixCdfFile.Rd
aroma.affymetrix/man/getAlleleProbePairs3.AffymetrixCdfFile.Rd
aroma.affymetrix/man/getFullName.Model.Rd
aroma.affymetrix/man/getDataSet.ArrayExplorer.Rd
aroma.affymetrix/man/allocateFromCdf.AffymetrixCelFile.Rd
aroma.affymetrix/man/UnitTypeScaleNormalization.Rd
aroma.affymetrix/man/AffymetrixCelSetReporter.Rd
aroma.affymetrix/man/getAverageFile.CnagCfhSet.Rd
aroma.affymetrix/man/GcContentNormalization.Rd
aroma.affymetrix/man/process.FragmentEquivalentClassNormalization.Rd
aroma.affymetrix/man/normalizeQuantile.AffymetrixCelFile.Rd
aroma.affymetrix/man/AffymetrixCelSetTuple.Rd
aroma.affymetrix/man/process.AbstractProbeSequenceNormalization.Rd
aroma.affymetrix/man/DChipDcpSet.Rd
aroma.affymetrix/man/process.LimmaBackgroundCorrection.Rd
aroma.affymetrix/man/getCnNames.AffymetrixCdfFile.Rd
aroma.affymetrix/man/AdditiveCovariatesNormalization.Rd
aroma.affymetrix/man/writeImage.AffymetrixCelFile.Rd
aroma.affymetrix/man/FragmentLengthNormalization.Rd
aroma.affymetrix/man/allocateFromCdf.AromaUnitTabularBinaryFile.Rd
aroma.affymetrix/man/createFrom.AffymetrixCelFile.Rd
aroma.affymetrix/man/getTimestamp.AffymetrixCelFile.Rd
aroma.affymetrix/man/groupUnitsByDimension.AffymetrixCdfFile.Rd
aroma.affymetrix/man/QualityAssessmentFile.Rd
aroma.affymetrix/man/AffymetrixCnChpSet.Rd
aroma.affymetrix/man/getChipType.CnagCfhFile.Rd
aroma.affymetrix/man/getOutputDataSet.TransformReport.Rd
aroma.affymetrix/man/getTags.GenericReporter.Rd
aroma.affymetrix/man/calculateBaseline.ChipEffectSet.Rd
aroma.affymetrix/man/getFullName.TransformReport.Rd
aroma.affymetrix/man/fromCdf.SnpInformation.Rd
aroma.affymetrix/man/FirmaSet.Rd
aroma.affymetrix/man/AffymetrixCelSet.Rd
aroma.affymetrix/man/AffymetrixFile.Rd
aroma.affymetrix/man/getFitUnitGroupFunction.FirmaModel.Rd
aroma.affymetrix/man/AffinePlm.Rd
aroma.affymetrix/man/getAlleleProbePairs.AffymetrixCdfFile.Rd
aroma.affymetrix/man/getIntensities.AffymetrixCelSet.Rd
aroma.affymetrix/man/getAlias.Model.Rd
aroma.affymetrix/man/SingleArrayUnitModel.Rd
aroma.affymetrix/man/LimmaBackgroundCorrection.Rd
aroma.affymetrix/man/getChipType.GenomeInformation.Rd
aroma.affymetrix/man/plotBoxplotStats.list.Rd
aroma.affymetrix/man/ScaleNormalization3.Rd
aroma.affymetrix/man/byChipType.AromaChipTypeAnnotationFile.Rd
aroma.affymetrix/man/fromDataFile.ChipEffectFile.Rd
aroma.affymetrix/man/createUniqueCdf.AffymetrixCdfFile.Rd
aroma.affymetrix/man/getCdf.AffymetrixCelSet.Rd
aroma.affymetrix/man/getFitUnitGroupFunction.RmaPlm.Rd
aroma.affymetrix/man/convertUnits.AffymetrixCdfFile.Rd
aroma.affymetrix/man/AffymetrixFileSet.Rd
aroma.affymetrix/man/findByChipType.AffymetrixPgfFile.Rd
aroma.affymetrix/man/getAlias.GenericReporter.Rd
aroma.affymetrix/man/SnpPlm.Rd
aroma.affymetrix/man/getData.SnpInformation.Rd
aroma.affymetrix/man/getCellIndices.ChipEffectFile.Rd
aroma.affymetrix/man/calculateResidualSet.FirmaModel.Rd
aroma.affymetrix/man/plotMvsA.AffymetrixCelFile.Rd
aroma.affymetrix/man/MultiArrayUnitModel.Rd
aroma.affymetrix/man/process.SpatialReporter.Rd
aroma.affymetrix/man/plotMvsX.AffymetrixCelFile.Rd
aroma.affymetrix/man/getXAM.ChipEffectSet.Rd
aroma.affymetrix/man/extractDataFrame.ParameterCelSet.Rd
aroma.affymetrix/man/ScaleNormalization.Rd
aroma.affymetrix/man/setTags.Model.Rd
aroma.affymetrix/man/UgpGenomeInformation.Rd
aroma.affymetrix/man/ChipEffectGroupMerge.Rd
aroma.affymetrix/man/AllelicCrosstalkCalibration.Rd
aroma.affymetrix/man/AvgPlm.Rd
aroma.affymetrix/man/ExonChipEffectSet.Rd
aroma.affymetrix/man/getResiduals.QualityAssessmentModel.Rd
aroma.affymetrix/man/getBaseline.ChipEffectSet.Rd
aroma.affymetrix/man/WeightsFile.Rd
aroma.affymetrix/man/getHeader.CnagCfhFile.Rd
aroma.affymetrix/man/getChipEffectSet.ProbeLevelModel.Rd
aroma.affymetrix/man/RmaBackgroundCorrection.Rd
aroma.affymetrix/man/nbrOfArrays.AffymetrixCelSet.Rd
aroma.affymetrix/man/importFromDChip.CnChipEffectSet.Rd
aroma.affymetrix/man/bpmapCluster2Cdf.Rd
aroma.affymetrix/man/isDuplicated.CnagCfhSet.Rd
aroma.affymetrix/man/getCellIndices.ResidualFile.Rd
aroma.affymetrix/man/getUnitIndices.GenomeInformation.Rd
aroma.affymetrix/man/getCdf.AffymetrixCelFile.Rd
aroma.affymetrix/man/setAlias.Model.Rd
aroma.affymetrix/man/doCRMAv2.Rd
aroma.affymetrix/man/ParameterCelSet.Rd
aroma.affymetrix/man/NormExpBackgroundCorrection.Rd
aroma.affymetrix/man/ChipEffectSet.Rd
aroma.affymetrix/man/getChipType.SnpInformation.Rd
aroma.affymetrix/man/DChipSnpInformation.Rd
aroma.affymetrix/man/writeCdf.AffyGenePDInfo.Rd
aroma.affymetrix/man/AffineSnpPlm.Rd
aroma.affymetrix/man/getTags.Model.Rd
aroma.affymetrix/man/AbstractProbeSequenceNormalization.Rd
aroma.affymetrix/man/readUnits.SingleArrayUnitModel.Rd
aroma.affymetrix/man/updateUnits.AffymetrixCelFile.Rd
aroma.affymetrix/man/LinearModelProbeSequenceNormalization.Rd
aroma.affymetrix/man/findUnitsTodo.FirmaModel.Rd
aroma.affymetrix/man/getFitUnitGroupFunction.SingleArrayUnitModel.Rd
aroma.affymetrix/man/findByChipType.AromaChipTypeAnnotationFile.Rd
aroma.affymetrix/man/BasePositionNormalization.Rd
aroma.affymetrix/man/getFitUnitGroupFunction.MultiArrayUnitModel.Rd
aroma.affymetrix/man/getProbeAffinityFile.ProbeLevelModel.Rd
aroma.affymetrix/man/getCellIndices.ProbeAffinityFile.Rd
aroma.affymetrix/man/process.MatSmoothing.Rd
aroma.affymetrix/man/process.DChipQuantileNormalization.Rd
aroma.affymetrix/man/compare.AffymetrixCdfFile.Rd
aroma.affymetrix/man/FirmaModel.Rd
aroma.affymetrix/man/as.character.AffymetrixCnChpSet.Rd
aroma.affymetrix/man/SmoothRmaModel.Rd
aroma.affymetrix/man/readRawData.AffymetrixCelFile.Rd
aroma.affymetrix/man/MbeiPlm.Rd
aroma.affymetrix/man/getChipType.AffymetrixCelSet.Rd
aroma.affymetrix/man/setCdf.AffymetrixCelFile.Rd
aroma.affymetrix/man/GenomeInformation.Rd
aroma.affymetrix/man/getCellIndices.ExonProbeAffinityFile.Rd
aroma.affymetrix/man/fitQuantileNormFcn.AffymetrixCelFile.Rd
aroma.affymetrix/man/getUnitIntensities.AffymetrixCelSet.Rd
aroma.affymetrix/man/setAlias.GenericReporter.Rd
aroma.affymetrix/man/as.character.DChipDcpSet.Rd
aroma.affymetrix/man/isResequenceChip.AffymetrixCdfFile.Rd
aroma.affymetrix/man/fromFile.AffymetrixCelFile.Rd
aroma.affymetrix/man/getFitUnitGroupFunction.AvgPlm.Rd
aroma.affymetrix/man/getDataSet.AffymetrixCelSetReporter.Rd
aroma.affymetrix/man/getFitUnitGroupFunction.MbeiPlm.Rd
aroma.affymetrix/man/getAverageFile.AffymetrixCelSet.Rd
aroma.affymetrix/man/AffymetrixProbeTabFile.Rd
aroma.affymetrix/man/extractAffyBatch.AffymetrixCelSet.Rd
aroma.affymetrix/man/findByChipType.AffymetrixCdfFile.Rd
aroma.affymetrix/man/setCdf.CnagCfhSet.Rd
aroma.affymetrix/man/ProbeLevelModel.Rd
aroma.affymetrix/man/getPath.TransformReport.Rd
aroma.affymetrix/man/findUnitsTodo.ProbeLevelModel.Rd
aroma.affymetrix/man/QualityAssessmentModel.Rd
aroma.affymetrix/man/GcContentNormalization2.Rd
aroma.affymetrix/man/process.ReseqCrosstalkCalibration.Rd
aroma.affymetrix/man/createMonocellCdf.AffymetrixCdfFile.Rd
aroma.affymetrix/man/verify.SnpInformation.Rd
aroma.affymetrix/man/fit.SmoothMultiarrayModel.Rd
aroma.affymetrix/man/doGCRMA.Rd
aroma.affymetrix/man/image270.AffymetrixCelFile.Rd
aroma.affymetrix/man/RmaPlm.Rd
aroma.affymetrix/man/AvgCnPlm.Rd
aroma.affymetrix/man/plotDensity.AffymetrixCelFile.Rd
aroma.affymetrix/man/process.ScaleNormalization3.Rd
aroma.affymetrix/man/process.QuantileNormalization.Rd
aroma.affymetrix/man/as.character.CnagCfhSet.Rd
aroma.affymetrix/man/QualityAssessmentSet.Rd
aroma.affymetrix/man/getCellIndices.UnitModel.Rd
aroma.affymetrix/man/smoothScatterMvsA.AffymetrixCelFile.Rd
aroma.affymetrix/man/getAM.ChipEffectFile.Rd
aroma.affymetrix/man/byChipType.UgpGenomeInformation.Rd
aroma.affymetrix/man/setCdf.AffymetrixCelSet.Rd
aroma.affymetrix/man/plotDensity.GenomeInformation.Rd
aroma.affymetrix/man/SpatialReporter.Rd
aroma.affymetrix/man/getDataSet.Model.Rd
aroma.affymetrix/man/AlleleSummation.Rd
aroma.affymetrix/man/ExonRmaPlm.Rd
aroma.affymetrix/man/fromFile.AffymetrixCdfFile.Rd
aroma.affymetrix/man/plotDensity.AffymetrixCelSet.Rd
aroma.affymetrix/man/DChipGenomeInformation.Rd
aroma.affymetrix/man/aroma.affymetrix-package.Rd
aroma.affymetrix/man/getCellIndices.ExonChipEffectFile.Rd
aroma.affymetrix/man/ParameterCelFile.Rd
aroma.affymetrix/man/getXAM.ChipEffectFile.Rd
aroma.affymetrix/man/getFitUnitGroupFunction.ExonRmaPlm.Rd
aroma.affymetrix/man/QuantileNormalization.Rd
aroma.affymetrix/man/process.BackgroundCorrection.Rd
aroma.affymetrix/man/readUnits.CnagCfhFile.Rd
aroma.affymetrix/man/getUnitGroupCellMap.ChipEffectFile.Rd
aroma.affymetrix/man/HetLogAddSnpPlm.Rd
aroma.affymetrix/man/getUnitNames.AffymetrixCdfFile.Rd
aroma.affymetrix/man/AffymetrixCelFile.Rd
aroma.affymetrix/man/BackgroundCorrection.Rd
aroma.affymetrix/man/CnChipEffectSet.Rd
aroma.affymetrix/man/getUnitNames.AffymetrixPgfFile.Rd
aroma.affymetrix/man/byChipType.DChipSnpInformation.Rd
aroma.affymetrix/man/process.UnitTypeScaleNormalization.Rd
aroma.affymetrix/man/MatNormalization.Rd
aroma.affymetrix/man/createExonByTranscriptCdf.AffymetrixCdfFile.Rd
aroma.affymetrix/man/isDuplicated.AffymetrixCelSet.Rd
aroma.affymetrix/man/OpticalBackgroundCorrection.Rd
aroma.affymetrix/man/process.RmaBackgroundCorrection.Rd
aroma.affymetrix/man/fromFile.CnagCfhFile.Rd
aroma.affymetrix/man/setRestructor.AffymetrixCdfFile.Rd
aroma.affymetrix/man/CnChipEffectFile.Rd
aroma.affymetrix/man/FirmaFile.Rd
aroma.affymetrix/man/ExonChipEffectFile.Rd
aroma.affymetrix/man/doCRMAv1.Rd
aroma.affymetrix/man/getCellIndices.SnpProbeAffinityFile.Rd
aroma.affymetrix/man/getUnitTypes.AffymetrixCdfFile.Rd
aroma.affymetrix/man/readUnits.AffymetrixCelFile.Rd
aroma.affymetrix/man/getHeader.AffymetrixCelFile.Rd
aroma.affymetrix/man/getName.GenericReporter.Rd
aroma.affymetrix/man/ProbeLevelTransform.Rd
aroma.affymetrix/man/MatSmoothing.Rd
aroma.affymetrix/man/getCellIndices.CnProbeAffinityFile.Rd
aroma.affymetrix/man/ChipEffectFile.Rd
aroma.affymetrix/man/nbrOfGroupsPerUnit.AffymetrixCdfFile.Rd
aroma.affymetrix/man/ResidualSet.Rd
aroma.affymetrix/man/fromCdf.GenomeInformation.Rd
aroma.affymetrix/man/ProbeAffinityFile.Rd
aroma.affymetrix/man/calculateParametersGsb.AffymetrixCelSet.Rd
aroma.affymetrix/man/getGenomeInformation.AffymetrixCdfFile.Rd
aroma.affymetrix/man/ArrayExplorer.Rd
aroma.affymetrix/man/UnitModel.Rd
aroma.affymetrix/man/normalizeQuantile.AffymetrixCelSet.Rd
aroma.affymetrix/man/getName.Model.Rd
aroma.affymetrix/man/SnpInformation.Rd
aroma.affymetrix/man/SmoothMultiarrayModel.Rd
aroma.affymetrix/man/getCellIndices.WeightsFile.Rd
aroma.affymetrix/man/process.ArrayExplorer.Rd
aroma.affymetrix/man/CnPlm.Rd
aroma.affymetrix/man/MbeiCnPlm.Rd
aroma.affymetrix/man/CrlmmParametersFile.Rd
aroma.affymetrix/man/plotImage.AffymetrixCelFile.Rd
aroma.affymetrix/man/doRMA.Rd
aroma.affymetrix/man/getCdf.Model.Rd
aroma.affymetrix/man/getWeights.QualityAssessmentModel.Rd
aroma.affymetrix/man/FragmentEquivalentClassNormalization.Rd
aroma.affymetrix/man/as.DChipDcpSet.DChipDcpSet.Rd
aroma.affymetrix/man/getTags.TransformReport.Rd
aroma.affymetrix/man/as.AffymetrixFileSet.AffymetrixFileSet.Rd
aroma.affymetrix/man/getChipEffectSet.AlleleSummation.Rd
aroma.affymetrix/man/readUnitsByQuartets.AffymetrixCdfFile.Rd
aroma.affymetrix/man/byChipType.SnpInformation.Rd
aroma.affymetrix/man/Non-documented_objects.Rd