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aroma.affymetrix (version 3.2.3)

Analysis of Large Affymetrix Microarray Data Sets

Description

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

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Version

Install

install.packages('aroma.affymetrix')

Monthly Downloads

719

Version

3.2.3

License

LGPL (>= 2.1)

Issues

8

Pull Requests

0

Stars

11

Forks

3

Maintainer

Henrik Bengtsson

Last Published

August 19th, 2025

Functions in aroma.affymetrix (3.2.3)

AffymetrixCdfFile

The AffymetrixCdfFile class
AffinePlm

The AffinePlm class
AffineSnpPlm

The AffineSnpPlm class
AffymetrixCelFile

The AffymetrixCelFile class
AffymetrixCelSetTuple

The AffymetrixCelSetTuple class
AdditiveCovariatesNormalization

The AdditiveCovariatesNormalization class
AffymetrixCelSetReporter

The AffymetrixCelSetReporter class
AffineCnPlm

The AffineCnPlm class
AffymetrixFile

The abstract AffymetrixFile class
ArrayExplorer

The ArrayExplorer class
AffymetrixFileSet

The AffymetrixFileSet class
AllelicCrosstalkCalibration

The AllelicCrosstalkCalibration class
AromaChipTypeAnnotationFile

The AromaChipTypeAnnotationFile class
AffymetrixCnChpSet

The AffymetrixCnChpSet class
AffymetrixPgfFile

The AffymetrixPgfFile class
AffymetrixProbeTabFile

The AffymetrixProbeTabFile class
AlleleSummation

The AlleleSummation class
AffymetrixFileSetReporter

The AffymetrixFileSetReporter class
BasePositionNormalization

The BasePositionNormalization class
ChipEffectGroupMerge

The ChipEffectGroupMerge class
AvgCnPlm

The AvgCnPlm class
AvgSnpPlm

The AvgSnpPlm class
AvgPlm

The AvgPlm class
BaseCountNormalization

The BaseCountNormalization class
ChipEffectTransform

The ChipEffectTransform class
BackgroundCorrection

The BackgroundCorrection class
ChipEffectSet

The ChipEffectSet class
ChipEffectFile

The ChipEffectFile class
CnagCfhFile

The CnagCfhFile class
DChipCdfBinFile

The DChipCdfBinFile class
CnChipEffectFile

The CnChipEffectFile class
CnProbeAffinityFile

The CnProbeAffinityFile class
CnPlm

The CnPlm class
CrlmmParametersFile

The CrlmmParametersFile class
CrlmmParametersSet

The CrlmmParametersSet class
CnChipEffectSet

The CnChipEffectSet class
DChipDcpFile

The DChipDcpFile class
CnagCfhSet

The CnagCfhSet class
ExonChipEffectFile

The ExonChipEffectFile class
FirmaFile

The FirmaFile class
ExonRmaPlm

The ExonRmaPlm class
ExonProbeAffinityFile

The ExonProbeAffinityFile class
FirmaModel

The FirmaModel class
DChipQuantileNormalization

The DChipQuantileNormalization class
ExonChipEffectSet

The ExonChipEffectSet class
DChipSnpInformation

The DChipSnpInformation class
DChipGenomeInformation

The DChipGenomeInformation class
DChipDcpSet

The DChipDcpSet class
FragmentEquivalentClassNormalization

The FragmentEquivalentClassNormalization class
GcRmaBackgroundCorrection

The GcRmaBackgroundCorrection class
GcContentNormalization2

The GcContentNormalization2 class
GenericReporter

The GenericReporter class
GcContentNormalization

The GcContentNormalization class
FragmentLengthNormalization

The FragmentLengthNormalization class
GenomeInformation

The GenomeInformation class
HetLogAddCnPlm

The HetLogAddCnPlm class
FirmaSet

The FirmaSet class
HetLogAddPlm

The HetLogAddPlm class
MatSmoothing

The MatSmoothing class
MbeiPlm

The MbeiPlm class
MbeiSnpPlm

The MbeiSnpPlm class
MultiArrayUnitModel

The MultiArrayUnitModel class
LimmaBackgroundCorrection

The LimmaBackgroundCorrection class
MatNormalization

The MatNormalization class
LinearModelProbeSequenceNormalization

The LinearModelProbeSequenceNormalization class
MbeiCnPlm

The MbeiCnPlm class
HetLogAddSnpPlm

The HetLogAddSnpPlm class
Model

The Model class
OpticalBackgroundCorrection

The OpticalBackgroundCorrection class
ProbeLevelTransform

The ProbeLevelTransform class
ParameterCelFile

The ParameterCelFile class
ParameterCelSet

The ParameterCelSet class
ProbeLevelModel

The ProbeLevelModel class
ProbeLevelTransform3

The ProbeLevelTransform3 class
Non-documented objects

Non-documented objects
RmaBackgroundCorrection

The RmaBackgroundCorrection class
QualityAssessmentSet

The QualityAssessmentSet class
QualityAssessmentModel

The QualityAssessmentModel class
RmaSnpPlm

The RmaSnpPlm class
ResidualFile

The ResidualFile class
QualityAssessmentFile

The QualityAssessmentFile class
NormExpBackgroundCorrection

The NormExpBackgroundCorrection class
RmaPlm

The RmaPlm class
ResidualSet

The ResidualSet class
ProbeAffinityFile

The ProbeAffinityFile class
RmaCnPlm

The RmaCnPlm class
QuantileNormalization

The QuantileNormalization class
ReseqCrosstalkCalibration

The ReseqCrosstalkCalibration class
SmoothMultiarrayModel

The SmoothMultiarrayModel class
SingleArrayUnitModel

The SingleArrayUnitModel class
SnpPlm

The SnpPlm interface class
SnpInformation

The SnpInformation class
SmoothRmaModel

The SmoothRmaModel class
SnpChipEffectSet

The SnpChipEffectSet class
ScaleNormalization3

The ScaleNormalization3 class
SnpChipEffectFile

The SnpChipEffectFile class
ScaleNormalization

The ScaleNormalization class
SnpChipEffectGroupMerge

The SnpChipEffectGroupMerge class
TransformReport

The TransformReport class
UnitModel

The UnitModel class
AffymetrixCelFile$allocateFromCdf

Creates an empty CEL file from a template CDF
AromaUnitTabularBinaryFile$allocateFromCdf

Creates an AromaUnitTabularBinaryFile mapping to a given CDF
WeightsSet

The WeightsSet class
SnpProbeAffinityFile

The SnpProbeAffinityFile class
SpatialReporter

The SpatialReporter class
UgpGenomeInformation

The UgpGenomeInformation class
UnitTypeScaleNormalization

The UnitTypeScaleNormalization class
aroma.affymetrix-package

Package aroma.affymetrix
GenomeInformation$byChipType

Static method to define a genome information set by chip type
as.CnagCfhSet.CnagCfhSet

Coerce an object to an CnagCfhSet object
as.AffymetrixCelSet.AffymetrixCelSet

Coerce an object to an AffymetrixCelSet object
WeightsFile

The WeightsFile class
as.AffymetrixCnChpSet.AffymetrixCnChpSet

Coerce an object to an AffymetrixCnChpSet object
as.character.DChipDcpSet

Returns a short string describing the DChip CHP set
bpmapCluster2Cdf

Creates a CDF from tiling-array BPMAP file
createFrom.AffymetrixCelFile

Creates a CEL file using another as a template
byChipType.SnpInformation

Static method to define a genome information set by chip type
as.character.CnagCfhSet

Returns a short string describing the CNAG CFH set
calculateBaseline.ChipEffectSet

Estimates the baseline signal chromosome by chromosome
byChipType.DChipSnpInformation

Defines a DChipSnpInformation object by chip type
averageQuantile.AffymetrixCelSet

Calculates the average empirical distribution across all samples
AromaChipTypeAnnotationFile$byChipType

Defines an AromaChipTypeAnnotationFile object by chip type
as.character.AffymetrixCnChpSet

Returns a short string describing the set
AffymetrixFileSet$byPath

Defines an AffymetrixFileSet object by searching for Affymetrix files
as.DChipDcpSet.DChipDcpSet

Coerce an object to an DChipDcpSet object
UgpGenomeInformation$byChipType

Defines a UgpGenomeInformation object by chip type
createMonocellCdf.AffymetrixCdfFile

Creates a mono-cell version of the CDF
computeAffinities.AffymetrixCdfFile

Calculates probe affinities from sequence
byChipType.DChipGenomeInformation

Defines a DChipGenomeInformation object by chip type
as.character.AffymetrixCelSet

Returns a short string describing the Affymetrix CEL set
createExonByTranscriptCdf.AffymetrixCdfFile

Creates an exon-by-transcript CDF
compare.AffymetrixCdfFile

Checks if two AffymetrixCdfFile objects are equal
calculateResidualSet.FirmaModel

Gets the set of residuals corresponding to the PLM
convertUnits.AffymetrixCdfFile

Gets and validates unit indices
as.AffymetrixFileSet.AffymetrixFileSet

Coerce an object to an AffymetrixFileSet object
convert.AffymetrixCdfFile

Converts a CDF into the same CDF but with another format
calculateParametersGsb.AffymetrixCelSet

Computes parameters for adjustment of specific binding
AffymetrixCelFile$clearData

Clears all or a subset of the fields in a CEL file
doCRMAv1

Estimation and assessment of raw copy numbers at the single locus level (CRMA v1)
extractFeatureSet.AffymetrixCelSet

Extracts CEL signals an in-memory FeatureSet object
doFIRMA

Finding Isoforms using Robust Multichip Analysis (FIRMA)
doGCRMA

Robust Multichip Analysis (GCRMA)
doCRMAv2

A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays (CRMA v2)
doRMA

Robust Multichip Analysis (RMA)
extractDataFrame.ParameterCelSet

Extract data as a data.frame for a set of arrays
extractExpressionSet.ChipEffectSet

Extracts an in-memory ExpressionSet object
createUniqueCdf.AffymetrixCdfFile

Creates a unique-cell version of the CDF
extractAffyBatch.AffymetrixCelSet

Extracts an in-memory AffyBatch object from the CEL set
extractMatrix.AffymetrixCelSet

Extract data as a matrix for a set of arrays
findUnitsTodo.ProbeLevelModel

Identifies non-fitted units
AffymetrixPgfFile$findByChipType

Locates a PGF file from its chip type
findUnitsTodo.UnitModel

Identifies non-fitted units
fit.Model

Estimates the model parameters
fit.FirmaModel

Estimates the model parameters
extractMatrix.ParameterCelSet

Extract data as a matrix for a set of arrays
findByChipType.AromaChipTypeAnnotationFile

Locates an annotation file by its chip type
AffymetrixCdfFile$findByChipType

Locates a CDF file from its chip type
AffymetrixCdfFile$fromFile

Defines an AffymetrixCdfFile object from a CDF file
fit.SingleArrayUnitModel

Estimates the model parameters
SnpInformation$fromCdf

Static method to define a genome information set from a CDF
GenomeInformation$fromCdf

Static method to define a genome information set from a CDF
findUnitsTodo.FirmaModel

Identifies non-fitted units
ChipEffectFile$fromDataFile

Retrieve an existing CEL file, or create from CDF template if missing
fit.SmoothMultiarrayModel

Fits the model for one chromosome across samples
fitQuantileNormFcn.AffymetrixCelFile

Fits quantile normalization functions for the arrays in the data set
AffymetrixPgfFile$fromFile

Defines an AffymetrixPgfFile object from a PGF file
fit.ProbeLevelModel

Estimates the model parameters
getAM.ChipEffectSet

Gets the log-intensities and log-ratios of chip effects of the set relative to a reference chip effect file
CnagCfhFile$fromFile

Defines an CnagCfhFile object from a CFH file
getAverageFile.AffymetrixCelSet

Calculates the mean and the standard deviation of the cell signal (intensity, standard deviation etc.) across the CEL set
AffymetrixCelFile$fromFile

Defines an AffymetrixCelFile object from a CEL file
getAlleleProbePairs3.AffymetrixCdfFile

Gets the indices of probepairs with the same pair of SNP nucleotides
getAM.ChipEffectFile

Gets the log-intensities and log-ratios of chip effects for two arrays
AromaChipTypeAnnotationFile$fromFile

Sets up an AromaChipTypeAnnotationFile
getAlias.GenericReporter

Gets the alias of the report
getAlleleCellPairs.AffymetrixCdfFile

Gets the cell indices of allele pairs
getAlleleProbePairs.AffymetrixCdfFile

Gets the indices of probepairs with the same pair of SNP nucleotides
getAverageFile.CnagCfhSet

Calculates the mean and the standard deviation of the cell signal (intensity, standard deviation etc.) across the CFH set
getCdf.AffymetrixCelSet

Gets the CDF structure for this CEL set
getAlias.Model

Gets the name alias for the model
getCdf.Model

Gets the CDF structure for this model
getCellIndices.CnChipEffectFile

Retrieves tree list of cell indices for a set of units
getCdf.CnagCfhSet

Gets the CDF structure for this CFH set
getCdf.CnagCfhFile

Gets the CDF structure for this CEL file
getCdf.AffymetrixCelFile

Gets the CDF structure for this CEL file
getCellIndices.ChipEffectFile

Retrieves tree list of cell indices for a set of units
getBaseline.ChipEffectSet

Gets the baseline signals across chromosomes
getCellIndices.AffymetrixCdfFile

Gets the cell indices unit by unit
getCellIndices.ExonProbeAffinityFile

Retrieves tree list of cell indices for a set of units
getCellIndices.UnitModel

Gets the cell indices unit by unit
getCellIndices.ExonChipEffectFile

Retrieves tree list of cell indices for a set of units
getCellIndices.WeightsFile

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.CnProbeAffinityFile

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.SnpChipEffectFile

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
getChipType.CnagCfhFile

Gets the chip type for this CEL file
getChipType.GenomeInformation

Gets the chip type of this genome information set
getData.SnpInformation

Gets all or a subset of the genome information data
getChipType.SnpInformation

Gets the chip type of this genome information set
getChipType.AffymetrixCelSet

Gets the chip type for this CEL set
getFitUnitGroupFunction.MbeiPlm

Gets the low-level function that fits the PLM
getDataSet.Model

Gets the input data set for this model
getData.GenomeInformation

Gets all or a subset of the genome information data
getChipType.AffymetrixCelFile

Gets the chip type for this CEL file
getChipEffectSet.AlleleSummation

Gets the set of chip effects for this model
getDataSet.ArrayExplorer

Gets the data set
getCnNames.AffymetrixCdfFile

Gets the names of the CN units
getChipEffectSet.ProbeLevelModel

Gets the set of chip effects for this model
MultiArrayUnitModel$getFitUnitGroupFunction

Static method to get the low-level function that fits the PLM
getFitUnitGroupFunction.AvgPlm

Gets the low-level function that fits the PLM
getHeader.AffymetrixCdfFile

Gets the header of the CDF file
getFirmaSet.FirmaModel

Gets the set of FIRMA results for this model
getFitUnitGroupFunction.AffinePlm

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
getDataSet.AffymetrixCelSetReporter

Gets the data set
getInputDataSet.TransformReport

Gets the source data set
getHeader.AffymetrixPgfFile

Gets the header of the PGF file
getName.TransformReport

Gets the name of the output data set
getFullName.TransformReport

Gets the full name of the output data set
getHeader.AffymetrixCelFile

Gets the header of the CEL file
getIntensities.AffymetrixCelSet

Gets cell intensities from a set of cells and a set of arrays
getName.Model

Gets the name of the output data set
getOutputDataSet.Transform

Gets the transformed data set
getHeader.AromaChipTypeAnnotationFile

Gets the header of the annotation file
SingleArrayUnitModel$getFitUnitGroupFunction

Static method to get the low-level function that fits the PLM
getPath.Model

Gets the path of this model
getHeader.CnagCfhFile

Gets the header of the CEL file
getName.GenericReporter

Gets the name of the explorer
getOutputDataSet.TransformReport

Gets the transformed data set
getTags.GenericReporter

Gets the tags of the reporter
getGenomeInformation.AffymetrixCdfFile

Gets genome information for this chip type
getFullName.Model

Gets the full name of the output set
getImage.AffymetrixCelFile

Creates an RGB Image object from a CEL file
getFitUnitGroupFunction.RmaPlm

Gets the low-level function that fits the PLM
getPositions.GenomeInformation

Gets the physical positions for a set of units
getPath.TransformReport

Gets the path of the output data set
getTags.TransformReport

Gets the tags of the output data set
getUnitIntensities.AffymetrixCelSet

Gets cell signals for a subset of units and a subset of arrays
getResiduals.QualityAssessmentModel

Calculates the residuals from a probe-level model
getTimestamp.AffymetrixCelFile

Gets the timestamp in the CEL header
getSnpNames.AffymetrixCdfFile

Gets the names of the SNP units
getUnitGroupCellMap.ChipEffectFile

Gets a (unit, group, cell) index map
getUnitNames.AffymetrixPgfFile

Gets the names of each unit
getUnitTypes.AffymetrixCdfFile

Gets the types of a set of units
getUnitNames.AffymetrixCdfFile

Gets the names of each unit
groupUnitsByDimension.AffymetrixCdfFile

Groups units by dimensions
getUnitIndices.GenomeInformation

Gets unit indices ordered along the chromosome
getRootPath.Model

Gets the root path of this model
getXAM.ChipEffectFile

Gets the physical position, log-intensities and log-ratios of chip effects for two arrays
AffymetrixCelSet$importFromDChip

Imports dChip-exported CEL files
getXAM.ChipEffectSet

Gets the physical position, log-intensities and log-ratios of chip effects for two arrays
getProbeAffinityFile.ProbeLevelModel

Gets the probe affinities for this model
getTags.Model

Gets the tags of the output data set
getWeights.QualityAssessmentModel

Calculates the weights from the robust fit to a probe-level model
isPm.AffymetrixCdfFile

Checks which cells (probes) are PMs and not
justRMA

Robust Multichip Analysis (RMA) reproducing the affy package
isSnpChip.AffymetrixCdfFile

Static method to check if a chip is a mapping (SNP) chip
CnChipEffectSet$importFromApt

Imports copy-number estimates from an APT summary file
image270.AffymetrixCelFile

Displays all or a subset of the data spatially
isDuplicated.CnagCfhSet

Identifies duplicated CFH files
isResequenceChip.AffymetrixCdfFile

Static method to check if a CDF is for a resequencing (CustomSeq) chip
isDuplicated.AffymetrixCelSet

Identifies duplicated CEL files
CnChipEffectSet$importFromDChip

Imports copy-number estimates from a dChip result file
nbrOfGroupsPerUnit.AffymetrixCdfFile

Gets the number of groups in each unit
plotDensity.AffymetrixCelFile

Plots the density of the probe signals on the array
plotDensity.GenomeInformation

Plots the density of SNPs for a given chromosome
plotImage.AffymetrixCelFile

Displays a spatial plot of a CEL file
plotBoxplotStats.list

Plots a (merged or non-merged) list of boxplot.stats() elements
nbrOfSnps.AffymetrixCdfFile

Gets the number of SNPs
normalizeQuantile.AffymetrixCelSet

Normalizes samples to have the same empirical distribution
plotDensity.AffymetrixCelSet

Plots the densities of all samples
normalizeQuantile.AffymetrixCelFile

Normalizes the probe intensities to a target empirical distribution
process.FragmentEquivalentClassNormalization

Normalizes the data set
process.DChipQuantileNormalization

Normalizes the data set
plotMvsA.AffymetrixCelFile

Plots log-ratio versus log-intensity in a scatter plot
process.BackgroundCorrection

Processes the data set
process.ArrayExplorer

Generates image files, scripts and dynamic pages for the explorer
process.AllelicCrosstalkCalibration

Calibrates the data set
process.MatSmoothing

Processes the data set
process.AbstractProbeSequenceNormalization

Normalizes the data set
process.AdditiveCovariatesNormalization

Normalizes the data set
process.MatNormalization

Normalizes the data set
process.ChipEffectGroupMerge

Normalizes the data set
process.LimmaBackgroundCorrection

Performs background correction
pdInfo2Cdf

Generates an Affymetrix CDF file from a Platform Design (PD) package and a auxiliary CEL file for the same chip type
process.QuantileNormalization

Normalizes the data set
process.ScaleNormalization3

Normalizes the data set
process.GenericReporter

Generates report
process.FragmentLengthNormalization

Normalizes the data set
process.OpticalBackgroundCorrection

Performs background correction
process.GcContentNormalization

Normalizes the data set
process.GcRmaBackgroundCorrection

Performs background correction
process.ReseqCrosstalkCalibration

Calibrates the data set
readUnits.AffymetrixCdfFile

Reads CDF data unit by unit
randomSeed

Sets and resets the .Random.seed in the global environment
process.SpatialReporter

Generates image files, scripts and dynamic pages for the explorer
setCdf.AffymetrixCelFile

Sets the CDF structure for this CEL file
setAlias.Model

Sets the name alias for the model
plotMvsX.AffymetrixCelFile

Plots log-ratio versus another variable in a scatter plot
process.ScaleNormalization

Normalizes the data set
process.RmaBackgroundCorrection

Performs background correction
setCdf.AffymetrixCelSet

Sets the CDF structure for this CEL set
setCdf.CnagCfhSet

Sets the CDF structure for this CFH set
setCdf.CnagCfhFile

Sets the CDF structure for this CEL file
readUnits.SingleArrayUnitModel

Reads data unit by unit
readUnits.MultiArrayUnitModel

Reads data unit by unit
setRestructor.AffymetrixCdfFile

Specifies a function through which
readUnitsByQuartets.AffymetrixCdfFile

Gets the cell quartets for each base position
readUnits.AffymetrixCelFile

Reads CEL data unit by unit
verify.GenomeInformation

Verifies the correctness of the underlying file
setArrays.ArrayExplorer

Sets the arrays
process.UnitTypeScaleNormalization

Normalizes the data set
updateUnits.AffymetrixCelFile

Updates CEL data unit by unit
readRawData.AffymetrixCelFile

Gets all or a subset of the fields in a CEL file
setAlias.GenericReporter

Sets the alias of the report
readUnits.CnagCfhFile

Reads CEL data unit by unit
writeImage.AffymetrixCelFile

Writes a spatial image of the signals in the CEL file
setTags.Model

Sets the tags to be appended
setupExampleData.AromaAffymetrix

Setups example data in the current directory
smoothScatterMvsA.AffymetrixCelFile

Plots log-ratio versus log-intensity in a smooth scatter plot
writeCdf.AffyGenePDInfo

Generates an Affymetrix CDF file from a Platform Design (PD) package
verify.SnpInformation

Verifies the correctness of the underlying file
AbstractProbeSequenceNormalization

The AbstractProbeSequenceNormalization class
AffymetrixCelSet

The AffymetrixCelSet class