aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

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.

AuthorHenrik Bengtsson [aut, cre, cph], James Bullard [ctb], Kasper Hansen [ctb], Pierre Neuvial [ctb], Elizabeth Purdom [ctb], Mark Robinson [ctb], Ken Simpson [ctb]
Date of publication2016-01-10 00:00:03
MaintainerHenrik Bengtsson <henrikb@braju.com>
LicenseLGPL (>= 2.1)
Version3.0.0
http://www.aroma-project.org/, https://github.com/HenrikBengtsson/aroma.affymetrix

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
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aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp
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aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp/21.doASCRMAv2,CalMaTe.R
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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
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aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/21.justRMA_vs_affy.R
aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping50K_Hind240
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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
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aroma.affymetrix/inst/testScripts/replication/chipTypes/Hs_PromPR_v02
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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
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aroma.affymetrix/inst/testScripts/parallel/chipTypes/Mapping10K_Xba142
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aroma.affymetrix/inst/testScripts/parallel/chipTypes/Mapping10K_Xba142/11a,doASCRMAv2.R
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aroma.affymetrix/inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/21.TCN,500K.R
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aroma.affymetrix/inst/testScripts/futures/GenomeWideSNP_6/11.AllelicCrosstalkCalibration.R
aroma.affymetrix/inst/testScripts/futures/HG-U133_Plus_2
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aroma.affymetrix/inst/testScripts/futures/HG-U133_Plus_2/12.GcRmaBackgroundCorrection.R
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aroma.affymetrix/inst/testScripts/futures/HG-U133_Plus_2/14.NormExpBackgroundCorrection.R
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aroma.affymetrix/inst/testScripts/futures/Hs_PromPR_v02
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aroma.affymetrix/inst/testScripts/futures/Mapping10K_Xba142
aroma.affymetrix/inst/testScripts/futures/Mapping10K_Xba142/11.UniqueCDF.R
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aroma.affymetrix/inst/testScripts/futures/Mapping10K_Xba142/11.AllelicCrosstalkCalibration.R
aroma.affymetrix/inst/testScripts/system
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aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6
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aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/11.justSNPRMA.R
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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
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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
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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
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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
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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
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aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240
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aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240/11.justSNPRMA.R
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aroma.affymetrix/inst/testScripts/system/chipTypes/MOUSEDIVm520650
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aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142
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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
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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
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aroma.affymetrix/inst/testScripts/complete
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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
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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
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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
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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
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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
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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
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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
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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
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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
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aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_5
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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
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aroma.affymetrix/inst/buildScripts/chipTypes/MOUSEDIVm520650
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aroma.affymetrix/inst/buildScripts/chipTypes/MOUSEDIVm520650/na30
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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
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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
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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
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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

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