To install this package, start R and enter:


In most cases, you don't need to download the package archive at all.


Methods for Affymetrix Oligonucleotide Arrays

Bioconductor version: 3.0

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

Author: Rafael A. Irizarry <rafa at>, Laurent Gautier <lgautier at>, Benjamin Milo Bolstad <bmb at>, and Crispin Miller <cmiller at> with contributions from Magnus Astrand <Magnus.Astrand at>, Leslie M. Cope <cope at>, Robert Gentleman, Jeff Gentry, Conrad Halling <challing at>, Wolfgang Huber, James MacDonald <jmacdon at>, Benjamin I. P. Rubinstein, Christopher Workman <workman at>, John Zhang

Maintainer: Rafael A. Irizarry <rafa at>

Citation (from within R, enter citation("affy")):


To install this package, start R and enter:



To view documentation for the version of this package installed in your system, start R and enter:



PDF R Script 1. Primer
PDF R Script 2. Built-in Processing Methods
PDF R Script 3. Custom Processing Methods
PDF R Script 4. Import Methods
PDF   Reference Manual
Text   NEWS


biocViews Microarray, OneChannel, Preprocessing, Software
Version 1.44.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier
License LGPL (>= 2.0)
Depends R (>= 2.8.0), BiocGenerics(>= 0.1.12), Biobase(>= 2.5.5)
Imports affyio(>= 1.13.3), BiocInstaller, graphics, grDevices, methods, preprocessCore, stats, utils, zlibbioc
LinkingTo preprocessCore
Suggests tkWidgets(>= 1.19.0), affydata, widgetTools
Depends On Me affyContam, affycoretools, affydata, AffyExpress, affyPara, affypdnn, affyPLM, affyQCReport, AffyRNADegradation, AgiMicroRna, ALLMLL, altcdfenvs, AmpAffyExample, arrayMvout, ArrayTools, bgx, bronchialIL13, ccTutorial, ChimpHumanBrainData, CLL, Cormotif, curatedBladderData, curatedOvarianData, DrugVsDisease, dualKS, ecoliLeucine, estrogen, ExiMiR, farms, frmaTools, gcrma, Hiiragi2013, LMGene, logitT, maPredictDSC, MAQCsubset, MAQCsubsetAFX, maskBAD, MLP, mvoutData, panp, plw, prebs, PREDAsampledata, puma, pumadata, qpcrNorm, ReadqPCR, RefPlus, rHVDM, Risa, RPA, SCAN.UPC, simpleaffy, SpikeIn, SpikeInSubset, sscore, Starr, webbioc, XhybCasneuf
Imports Me affyILM, affylmGUI, affyQCReport, AffyTiling, ArrayExpress, arrayQualityMetrics, ArrayTools, CAFE, ChIPXpress, Cormotif, DeSousa2013, farms, ffpe, frma, gcrma, GEOsubmission, Harshlight, HTqPCR, lumi, LVSmiRNA, makecdfenv, MSnbase, PECA, plier, plw, puma, pvac, Rnits, simpleaffy, tilingArray, TurboNorm, vsn, waveTiling
Suggests Me AnnotationForge, beadarray, beadarraySNP, BiocCaseStudies, BiocGenerics, Biostrings, BufferedMatrixMethods, categoryCompare, ecolitk, estrogen, ExpressionView, factDesign, ffpeExampleData, gCMAPWeb, GeneRegionScan, limma, made4, MLSeq, oneChannelGUI, paxtoolsr, piano, PREDA, prot2D, qcmetrics, siggenes
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source affy_1.44.0.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) affy_1.44.0.tgz
Mac OS X 10.9 (Mavericks) affy_1.44.0.tgz
Browse/checkout source (username/password: readonly)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center