affy
This is the released version of affy; for the devel version, see affy.
All Bioconductor versions of affy
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5
Methods for Affymetrix Oligonucleotide Arrays
Bioconductor version: 3.23 · Package version: 1.90.0
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 ds.dfci.harvard.edu>, Laurent Gautier <lgautier at gmail.com>, Benjamin Milo Bolstad <bmb at bmbolstad.com>, and Crispin Miller <cmiller at picr.man.ac.uk> with contributions from Magnus Astrand <Magnus.Astrand at astrazeneca.com>, Leslie M. Cope <cope at mts.jhu.edu>, Robert Gentleman, Jeff Gentry, Conrad Halling <challing at agilixcorp.com>, Wolfgang Huber, James MacDonald <jmacdon at u.washington.edu>, Benjamin I. P. Rubinstein, Christopher Workman <workman at cbs.dtu.dk>, John Zhang
Maintainer: Robert D. Shear <rshear at ds.dfci.harvard.edu>
Citation
From within R, enter citation("affy"):
Rafael A. Irizarry, Laurent Gautier, Benjamin Milo Bolstad, and Crispin Miller with contributions from Magnus Astrand, Leslie M. Cope, Robert Gentleman, Jeff Gentry, Conrad Halling, Wolfgang Huber, James MacDonald, Benjamin I. P. Rubinstein, Christopher Workman, John Zhang. affy: Methods for Affymetrix Oligonucleotide Arrays. doi:10.18129/B9.bioc.affy, R package version 1.90.0, https://bioconductor.org/packages/affy.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("affy")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.90.0 |
| License | LGPL (>= 2.0) |
| URL | https://bioconductor.org/packages/affy |
| Bug Reports | https://github.com/rafalab/affy/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 2.5 or earlier (R-2.10) (16 years) |
| Downloads rank | 77 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Microarray, OneChannel, Preprocessing, Software |
| Package Short Url | https://bioconductor.org/packages/affy/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("affy")| Primer | R Script | |
| Built-in Processing Methods | R Script | |
| Custom Processing Methods | R Script | |
| Import Methods | R Script | |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | affy_1.90.0.tar.gz |
| Windows binary (x86_64) | affy_1.90.0.zip |
| macOS binary (arm64) | affy_1.90.0.tgz |
| macOS binary (x86_64) | affy_1.90.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/affy |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/affy |
| Package Downloads Report | Download Stats |
Dependencies
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
LinkingTo: preprocessCore
Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools, hgu95av2cdf
Reverse dependencies
Depends On Me (33): affyContam, affydata, affyPLM, AffyRNADegradation, AgiMicroRna, ALLMLL, altcdfenvs, AmpAffyExample, arrayMvout, bronchialIL13, ChimpHumanBrainData, CLL, Cormotif, curatedBladderData, DrugVsDisease, ecoliLeucine, ExiMiR, frmaTools, gcrma, maPredictDSC, MAQCsubset, maskBAD, mvoutData, panp, prebs, PREDAsampledata, qpcrNorm, RPA, SCAN.UPC, SpikeIn, SpikeInSubset, webbioc, XhybCasneuf
Imports Me (32): affycoretools, affyILM, affylmGUI, arrayQualityMetrics, bnem, CAFE, ChIPXpress, Cormotif, DeSousa2013, Doscheda, ffpe, frma, gcrma, GEOsubmission, HTqPCR, iCheck, lumi, makecdfenv, mimager, MSnbase, PECA, plier, puma, pvac, rat2302frmavecs, rCGH, Rnits, signatureSearchData, STATegRa, tilingArray, TurboNorm, vsn
Suggests Me (27): AnnotationForge, aroma.affymetrix, ArrayExpress, arrays, ath1121501frmavecs, autonomics, beadarray, BiocGenerics, Biostrings, BufferedMatrixMethods, categoryCompare, ecolitk, estrogen, factDesign, ffpeExampleData, GeneRegionScan, hexbin, Hiiragi2013, isatabr, limma, made4, maGUI, piano, PREDA, qcmetrics, siggenes, TCGAbiolinks