affy

Methods for Affymetrix Oligonucleotide Arrays

Bioconductor version: 2.9

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 med.umich.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
Depends	R (>= 2.8.0), Biobase(>= 2.5.5)
Imports	affyio(>= 1.13.3), Biobase(>= 2.5.5), BiocInstaller, graphics, grDevices, methods, preprocessCore, stats, utils, zlibbioc
Suggests	tkWidgets(>= 1.19.0), affydata
System Requirements
License	LGPL (>= 2.0)
URL
Depends On Me	affyContam, affycoretools, affydata, AffyExpress, affylmGUI, affyPara, affypdnn, affyPLM, affyQCReport, AgiMicroRna, ALLMLL, altcdfenvs, AmpAffyExample, arrayMvout, ArrayTools, bgx, bronchialIL13, CLL, Cormotif, dualKS, ecoliLeucine, estrogen, ExiMiR, farms, frmaTools, gcrma, LMGene, logitT, LVSmiRNA, maDB, MAQCsubset, MAQCsubsetAFX, MLP, mvoutData, panp, plw, PREDAsampledata, puma, pumadata, qpcrNorm, ReadqPCR, RefPlus, rHVDM, RPA, simpleaffy, SpikeIn, SpikeInSubset, sscore, Starr, webbioc, XhybCasneuf
Imports Me	affyILM, affyQCReport, AffyTiling, ArrayExpress, arrayQualityMetrics, ArrayTools, Cormotif, 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, ffpeExampleData, GeneRegionScan, limma, made4, oneChannelGUI, PREDA, siggenes, TurboNorm
Version	1.32.1
Since	Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source	affy_1.32.1.tar.gz
Windows Binary	affy_1.32.1.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	affy_1.32.1.tgz
Package Downloads Report	Download Stats

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