Package: affy 1.91.0

Robert D. Shear

affy: Methods for Affymetrix Oligonucleotide Arrays

The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.

Authors:Rafael A. Irizarry <[email protected]>, Laurent Gautier <[email protected]>, Benjamin Milo Bolstad <[email protected]>, and Crispin Miller <[email protected]> with contributions from Magnus Astrand <[email protected]>, Leslie M. Cope <[email protected]>, Robert Gentleman, Jeff Gentry, Conrad Halling <[email protected]>, Wolfgang Huber, James MacDonald <[email protected]>, Benjamin I. P. Rubinstein, Christopher Workman <[email protected]>, John Zhang

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manual.pdf |manual.html✨
card.svg |card.png
affy/json (API)
NEWS

# Install 'affy' in R:
install.packages('affy', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rafalab/affy/issues

Datasets:

On BioConductor:affy-1.91.0(bioc 3.24)affy-1.90.0(bioc 3.23)

microarrayonechannelpreprocessing

12.44 score 106 packages 2.1k scripts 13k downloads 989 mentions 123 exports 6 dependencies

Last updated from:899ad50ee3. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR153
linux-devel-arm64WARNING197
linux-devel-x86_64WARNING216
source / vignettesOK253
linux-release-arm64WARNING188
linux-release-x86_64WARNING227
macos-release-arm64WARNING129
macos-release-x86_64WARNING292
macos-oldrel-arm64WARNING125
macos-oldrel-x86_64WARNING307
windows-develWARNING522
windows-releaseWARNING544
windows-oldrelWARNING518
wasm-releaseOK132

Exports:.setAffyOptions$.AffyBatchaffy.scalevalue.exprSetAffyRNAdegAllButCelsForReadAffyavdiffbarplotbarplot.ProbeSetbg.adjustbg.correctbg.correct.masbg.correct.nonebg.correct.rmabg.parametersbgcorrect.methodsboxplotcdfFromBioCcdfFromEnvironmentcdfFromLibPathcdfNamecheckValidFilenamescleancdfnameclosecomputeExprSetdebug.affy123express.summary.statexpress.summary.stat.methodsexpressoexpressoWidgetexprsexprs<-featureNamesfit.li.wonggeneNamesgenerateExprSet.methodsgenerateExprVal.method.avgdiffgenerateExprVal.method.liwonggenerateExprVal.method.masgenerateExprVal.method.medianpolishgenerateExprVal.method.playeroutgetCdfInfohisthlogimageindexProbesindices2xyintensityintensity<-just.rmajustRMAli.wonglist.celfilesloess.normalizema.plotmaffy.normalizemaffy.subsetMAplotmas5mas5.detectionmas5callsmas5calls.AffyBatchmas5calls.ProbeSetMboxmedianpolishmerge.AffyBatchmmmm<-mmindexmultiloessmva.pairsnormalize.AffyBatch.constantnormalize.AffyBatch.contrastsnormalize.AffyBatch.invariantsetnormalize.AffyBatch.loessnormalize.AffyBatch.methodsnormalize.AffyBatch.qsplinenormalize.AffyBatch.quantilesnormalize.AffyBatch.quantiles.robustnormalize.constantnormalize.invariantsetnormalize.loessnormalize.methodsnormalize.qsplineopenpairs.AffyBatchplayerout.costfunctionplot.ProbeSetplotAffyRNAdegplotDensityplotDensity.AffyBatchplotLocationpmpm<-pmcorrect.maspmcorrect.methodspmcorrect.pmonlypmcorrect.subtractmmpmindexppset.ttestppsetApplyprobeNamesprobesprobesetread.affybatchread.probematrixReadAffyrmasampleNamesse.exprsshowsimplemultiLoesssummaryAffyRNAdegtukey.biweighttukeybiweightupDate.bgcorrect.methodsupDate.express.summary.stat.methodsupDate.generateExprSet.methodsupDate.normalize.AffyBatch.methodsupDate.pmcorrect.methodsupdateMeupdateObjectwhatcdfxy2indices

Dependencies:affyioBiobaseBiocGenericsBiocManagergenericspreprocessCore

Primer

Rendered fromaffy.Rnwusingutils::Sweaveon May 25 2026.

Last update: 2013-10-12
Started: 2013-10-12

Built-in Processing Methods

Rendered frombuiltinMethods.Rnwusingutils::Sweaveon May 25 2026.

Last update: 2013-10-12
Started: 2013-10-12

Custom Processing Methods

Rendered fromcustomMethods.Rnwusingutils::Sweaveon May 25 2026.

Last update: 2013-10-12
Started: 2013-10-12

Import Methods

Rendered fromvim.Rnwusingutils::Sweaveon May 25 2026.

Last update: 2013-10-12
Started: 2013-10-12

Readme and manuals

Help Manual

Help pageTopics
~~function to set options ~~.setAffyOptions
Deprecated functions in package 'affy'loess.normalize maffy.normalize multiloess simplemultiLoess
Options for the affy packageaffy-options
Scale normalization for expreSetsaffy.scalevalue.exprSet
Class AffyBatch$.AffyBatch AffyBatch AffyBatch,ANY AffyBatch-class bg.correct,AffyBatch,character-method boxplot,AffyBatch-method cdfName cdfName,AffyBatch-method checkValidFilenames col,AffyBatch-method computeExprSet,AffyBatch,character,character-method dim,AffyBatch-method exprs,AffyBatch-method exprs<-,AffyBatch,ANY-method featureNames,AffyBatch-method featureNames<-,AffyBatch-method geneNames geneNames,AffyBatch-method geneNames<- geneNames<-,AffyBatch,ANY-method getCdfInfo getCdfInfo,AffyBatch-method hist,AffyBatch-method image image,AffyBatch-method indexProbes indexProbes,AffyBatch,character-method indexProbes,AffyBatch,missing-method indexProbes,AffyBatch-method initialize,AffyBatch-method intensity intensity,AffyBatch-method intensity<- intensity<-,AffyBatch-method length,AffyBatch-method mm,AffyBatch-method mm<-,AffyBatch,ANY-method mmindex mmindex,AffyBatch-method pm,AffyBatch-method pm<-,AffyBatch,ANY-method pmindex pmindex,AffyBatch-method probeNames,AffyBatch-method probes probes,AffyBatch-method probeset probeset,AffyBatch-method row,AffyBatch-method se.exprs,AffyBatch-method se.exprs<-,AffyBatch-method show,AffyBatch-method updateObject,AffyBatch-method [,AffyBatch-method [<-,AffyBatch-method [[,AffyBatch-method
Function to assess RNA degradation in Affymetrix GeneChip data.AffyRNAdeg plotAffyRNAdeg summaryAffyRNAdeg
show a ProbeSet as barplotsbarplot.ProbeSet
Background adjustment (internal function)bg.adjust bg.parameters
Background Correctionbg.correct bg.correct.mas bg.correct.none bg.correct.rma
Example cdfenvcdfenv.example
Functions to obtain CDF filescdfFromBioC cdfFromEnvironment cdfFromLibPath
Clean Affymetrix's CDF namecleancdfname mapCdfName
Debugging Flagdebug.affy123
From raw probe intensities to expression valuesbgcorrect expresso
A widget for users to pick correction methodsexpressoWidget
Fit Li and Wong Model to a Probe Setfit.li.wong li.wong
generate a set of expression valuescomputeExprSet generateExprSet-methods generateExprSet.methods upDate.generateExprSet.methods
Compute a summary expression value from the probes intensitiesexpress.summary.stat express.summary.stat-methods express.summary.stat.methods upDate.express.summary.stat.methods
Generate an expression value from the probes informationsgenerateExprVal.method.avgdiff generateExprVal.method.liwong generateExprVal.method.mas generateExprVal.method.medianpolish
Generate an expression value from the probes informationsgenerateExprVal.method.playerout playerout.costfunction
Hybrid Loghlog
Read CEL files into an ExpressionSetjust.rma justRMA
List the Cel Files in a Directory/Folderlist.celfiles
Relative M vs. A plotsma.plot MAplot MAplot,AffyBatch-method Mbox Mbox,AffyBatch-method
MAS 5.0 expression measuremas5
MAS 5.0 Absolute Detectionmas5.detection mas5calls mas5calls,AffyBatch-method mas5calls,ProbeSet-method mas5calls.AffyBatch mas5calls.ProbeSet
merge two AffyBatch objectsmerge.AffyBatch
M vs. A Matrixmva.pairs
Normalize Affymetrix Probe Level Data - methodsbgcorrect.methods normalize,AffyBatch-method normalize.AffyBatch normalize.AffyBatch.methods normalize.methods normalize.methods,AffyBatch-method pmcorrect.methods upDate.bgcorrect.methods upDate.normalize.AffyBatch.methods upDate.pmcorrect.methods
Scale probe intensitiesnormalize.AffyBatch.constant normalize.constant
Normalize intensities using the contrasts methodnormalize.AffyBatch.contrasts normalize.contrasts
Invariant Set normalizationnormalize.AffyBatch.invariantset normalize.invariantset
Scale microarray datanormalize.AffyBatch.loess normalize.loess
Normalize arraysnormalize.AffyBatch.qspline normalize.qspline qspline-normalize
Quantile Normalizationnormalize.AffyBatch.quantiles
Robust Quantile Normalizationnormalize.AffyBatch.quantiles.robust
plot intensities using 'pairs'pairs.AffyBatch
plot a probe setplot.ProbeSet
Plot DensitiesplotDensity plotDensity.AffyBatch
Plot a location on a cel imageplotLocation
PM Correctionpmcorrect pmcorrect.mas pmcorrect.pmonly pmcorrect.subtractmm
Apply a function over the ProbeSets in an AffyBatchppset.ttest ppsetApply
Methods for accessing perfect matches and mismatchesmm mm<- pm pm<- probeMatch probeMatch-methods
Methods for accessing the Probe NamesprobeNames probeNames-methods probeNames<-
Class ProbeSetbarplot,ProbeSet-method colnames,ProbeSet-method express.summary.stat,ProbeSet,character,character-method mm,ProbeSet-method mm<-,ProbeSet,matrix-method pm,ProbeSet-method pm<-,ProbeSet,matrix-method ProbeSet-class sampleNames,ProbeSet-method show,ProbeSet-method
Class "ProgressBarText"close,ProgressBarText-method initialize,ProgressBarText-method open,ProgressBarText-method ProgressBarText-class updateMe updateMe,ProgressBarText-method
Read CEL files into an AffyBatchAllButCelsForReadAffy read.affybatch ReadAffy
Read CEL file data into PM or MM matricesread.probematrix
Robust Multi-Array Average expression measurerma
SpikeIn Experiment Data: ProbeSet Exampleconcentrations SpikeIn
Probe Set Summarizing Functionsavdiff medianpolish summary tukeybiweight
One-step Tukey's biweighttukey.biweight
Find which CDF correspondswhatcdf
Functions to convert indices to x/y (and reverse)indices2xy xy2indices