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This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see affy.

Methods for Affymetrix Oligonucleotide Arrays

Bioconductor version: 2.8

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")):


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PDF affy.pdf
PDF builtinMethods.pdf
PDF customMethods.pdf
PDF vim.pdf
PDF   Reference Manual


biocViews Microarray, OneChannel, Preprocessing, Software
Version 1.30.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 11 years)
License LGPL (>= 2.0)
Depends R (>= 2.8.0), Biobase(>= 2.5.5)
Imports affyio(>= 1.13.3), Biobase(>= 2.5.5), graphics, grDevices, methods, preprocessCore, stats, utils
LinkingTo preprocessCore
Suggests tkWidgets(>= 1.19.0), affydata
Depends On Me affyContam, affycoretools, affydata, AffyExpress, affylmGUI, affyPara, affypdnn, affyPLM, affyQCReport, AgiMicroRna, ALLMLL, altcdfenvs, AmpAffyExample, arrayMvout, ArrayTools, bgx, bronchialIL13, ccTutorial, CLL, dualKS, ecoliLeucine, estrogen, ExiMiR, farms, frmaTools, gcrma, LMGene, logitT, LVSmiRNA, maDB, MAQCsubset, MAQCsubsetAFX, MLP, mvoutData, panp, plw, puma, pumadata, qpcrNorm, RefPlus, rHVDM, RPA, simpleaffy, SpikeIn, SpikeInSubset, sscore, Starr, webbioc, XhybCasneuf
Imports Me affyILM, affyQCReport, AffyTiling, ArrayExpress, arrayQualityMetrics, ArrayTools, farms, frma, gcrma, GEOsubmission, Harshlight, HTqPCR, lumi, makecdfenv, plier, plw, puma, pvac, simpleaffy, tilingArray, TurboNorm, vsn
Suggests Me AnnotationDbi, beadarray, beadarraySNP, BiocCaseStudies, Biostrings, BufferedMatrixMethods, estrogen, ExpressionView, factDesign, GeneRegionScan, hexbin, limma, made4, oneChannelGUI, siggenes, TurboNorm
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