DOI: 10.18129/B9.bioc.affy  

Methods for Affymetrix Oligonucleotide Arrays

Bioconductor version: Release (3.17)

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: Robert D. Shear <rshear at>

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


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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 1.78.2
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 18.5 years)
License LGPL (>= 2.0)
Depends R (>= 2.8.0), BiocGenerics(>= 0.1.12), Biobase(>= 2.5.5)
Imports affyio(>= 1.13.3), BiocManager, graphics, grDevices, methods, preprocessCore, stats, utils, zlibbioc
LinkingTo preprocessCore
Suggests tkWidgets(>= 1.19.0), affydata, widgetTools, hgu95av2cdf
Depends On Me affyContam, affydata, affyPLM, AffyRNADegradation, AgiMicroRna, ALLMLL, altcdfenvs, AmpAffyExample, arrayMvout, bgx, bronchialIL13, ccTutorial, ChimpHumanBrainData, CLL, Cormotif, curatedBladderData, curatedOvarianData, DrugVsDisease, ecoliLeucine, ExiMiR, farms, frmaTools, gcrma, Hiiragi2013, logitT, maPredictDSC, MAQCsubset, maskBAD, mvoutData, panp, prebs, PREDAsampledata, qpcrNorm, RefPlus, Risa, RPA, SCAN.UPC, SpikeIn, SpikeInSubset, sscore, webbioc, XhybCasneuf
Imports Me affycoretools, affyILM, affylmGUI, arrayQualityMetrics, bnem, CAFE, ChIPXpress, Cormotif, crossmeta, DeSousa2013, Doscheda, farms, ffpe, frma, gcrma, GEOsubmission, Harshlight, HTqPCR, iCheck, lumi, makecdfenv, mimager, MSnbase, PECA, plier, puma, pvac, rat2302frmavecs, rCGH, Rnits, signatureSearchData, STATegRa, tilingArray, TurboNorm, vsn
Suggests Me AnnotationForge, ArrayExpress, arrays, autonomics, beadarray, beadarraySNP, BiocGenerics, Biostrings, BufferedMatrixMethods, categoryCompare, ecolitk, estrogen, factDesign, ffpeExampleData, GeneRegionScan, limma, made4, piano, PREDA, qcmetrics, runibic, siggenes, TCGAbiolinks
Links To Me
Build Report  

Package Archives

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

Source Package affy_1.78.2.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) affy_1.78.2.tgz
macOS Binary (arm64) affy_1.78.2.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: