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Bioconductor - affy

affy

This is the released version of affy; for the devel version, see affy.

Methods for Affymetrix Oligonucleotide Arrays

Bioconductor version: Release (3.21)

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")): Installation

To install this package, start R (version "4.5") 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.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("affy")

Details biocViews Microarray, OneChannel, Preprocessing, Software Version 1.86.0 In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 20 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 System Requirements URL https://bioconductor.org/packages/affy Bug Reports https://github.com/rafalab/affy/issues See More Suggests tkWidgets(>= 1.19.0), affydata, widgetTools, hgu95av2cdf Linking To preprocessCore Enhances Depends On Me affyContam, affyPLM, AffyRNADegradation, altcdfenvs, arrayMvout, 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, Doscheda, ffpe, frma, gcrma, GEOsubmission, Harshlight, HTqPCR, iCheck, lumi, makecdfenv, mimager, MSnbase, PECA, plier, puma, pvac, Rnits, STATegRa, tilingArray, TurboNorm, vsn, rat2302frmavecs, DeSousa2013, signatureSearchData, bapred 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 Build Report Build Report Package Archives

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

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