affy

Methods for Affymetrix Oligonucleotide Arrays

Bioconductor version: Development (3.0)

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 jhu.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: Rafael A. Irizarry <rafa at jhu.edu>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("affy")

To cite this package in a publication, start R and enter:

    citation("affy")

Documentation

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
Text   NEWS

Details

biocViews Microarray, OneChannel, Preprocessing, Software
Version 1.43.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier
License LGPL (>= 2.0)
Depends R (>= 2.8.0), BiocGenerics(>= 0.1.12), Biobase(>= 2.5.5)
Imports affyio(>= 1.13.3), BiocInstaller, graphics, grDevices, methods, preprocessCore, stats, utils, zlibbioc
Suggests tkWidgets(>= 1.19.0), affydata, widgetTools
System Requirements
URL
Depends On Me affyContam, affycoretools, affydata, AffyExpress, affylmGUI, affylmGUI, affyPara, affypdnn, affyPLM, affyQCReport, AffyRNADegradation, AgiMicroRna, ALLMLL, altcdfenvs, AmpAffyExample, arrayMvout, ArrayTools, bgx, bronchialIL13, ccTutorial, ChimpHumanBrainData, CLL, Cormotif, curatedBladderData, curatedOvarianData, DrugVsDisease, dualKS, ecoliLeucine, estrogen, ExiMiR, farms, frmaTools, gcrma, Hiiragi2013, LMGene, logitT, maPredictDSC, MAQCsubset, MAQCsubsetAFX, maskBAD, MLP, mvoutData, panp, plw, prebs, PREDAsampledata, puma, pumadata, qpcrNorm, ReadqPCR, RefPlus, rHVDM, Risa, RPA, SCAN.UPC, simpleaffy, SpikeIn, SpikeInSubset, sscore, Starr, webbioc, XhybCasneuf
Imports Me affyILM, affyQCReport, AffyTiling, ArrayExpress, arrayQualityMetrics, ArrayTools, CAFE, ChIPXpress, Cormotif, DeSousa2013, farms, ffpe, frma, gcrma, GEOsubmission, Harshlight, HTqPCR, lumi, LVSmiRNA, makecdfenv, MSnbase, PECA, plier, plw, puma, pvac, simpleaffy, tilingArray, TurboNorm, virtualArray, vsn, waveTiling
Suggests Me AnnotationForge, beadarray, beadarraySNP, BiocCaseStudies, BiocGenerics, Biostrings, BufferedMatrixMethods, categoryCompare, ecolitk, estrogen, ExpressionView, factDesign, ffpeExampleData, gCMAPWeb, GeneRegionScan, limma, made4, MLSeq, oneChannelGUI, piano, PREDA, prot2D, qcmetrics, siggenes

Package Downloads

Package Source affy_1.43.0.tar.gz
Windows Binary affy_1.43.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) affy_1.43.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

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