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>

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To cite this package in a publication, 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


biocViews Microarray, OneChannel, Preprocessing
Depends R (>= 2.8.0), Biobase(>= 2.5.5)
Imports affyio(>= 1.13.3), Biobase(>= 2.5.5), graphics, grDevices, methods, preprocessCore, stats, utils
Suggests tkWidgets(>= 1.19.0), affydata
System Requirements
License LGPL (>= 2.0)
Depends On Me affyContam, affycoretools, affydata, AffyExpress, affylmGUI, affyPara, affypdnn, affyPLM, affyQCReport, AgiMicroRna, ALLMLL, altcdfenvs, AmpAffyExample, arrayMvout, ArrayTools, bgx, bronchialIL13, 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
Version 1.30.0
Since Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source affy_1.30.0.tar.gz
Windows Binary (32- & 64-bit)
MacOS 10.5 (Leopard) binary affy_1.30.0.tgz
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