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Methods for Affymetrix Oligonucleotide Arrays

Bioconductor version: Release (3.19)

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 "4.4") 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:

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


biocViews Microarray, OneChannel, Preprocessing, Software
Version 1.82.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 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
System Requirements
Bug Reports
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Suggests tkWidgets(>= 1.19.0), affydata, widgetTools, hgu95av2cdf
Linking To preprocessCore
Depends On Me affyContam, affyPLM, AffyRNADegradation, altcdfenvs, arrayMvout, bgx, Cormotif, DrugVsDisease, ExiMiR, frmaTools, gcrma, maskBAD, panp, prebs, qpcrNorm, RPA, SCAN.UPC, webbioc, affydata, ALLMLL, AmpAffyExample, bronchialIL13, CLL, curatedBladderData, ecoliLeucine, Hiiragi2013, MAQCsubset, mvoutData, PREDAsampledata, SpikeIn, SpikeInSubset, XhybCasneuf, RobLoxBioC
Imports Me affycoretools, affyILM, affylmGUI, arrayQualityMetrics, bnem, CAFE, ChIPXpress, Cormotif, crossmeta, Doscheda, ffpe, frma, gcrma, GEOsubmission, Harshlight, iCheck, lumi, makecdfenv, mimager, MSnbase, PECA, plier, puma, pvac, Rnits, STATegRa, tilingArray, TurboNorm, vsn, rat2302frmavecs, DeSousa2013, signatureSearchData, bapred, seeker
Suggests Me AnnotationForge, ArrayExpress, autonomics, beadarray, BiocGenerics, Biostrings, BufferedMatrixMethods, categoryCompare, ecolitk, factDesign, GeneRegionScan, limma, made4, piano, PREDA, qcmetrics, runibic, siggenes, TCGAbiolinks, ath1121501frmavecs, estrogen, ffpeExampleData, arrays, aroma.affymetrix, hexbin, isatabr, maGUI
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package affy_1.82.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) affy_1.82.0.tgz
macOS Binary (arm64) affy_1.82.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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