affy

Methods for Affymetrix Oligonucleotide Arrays

Bioconductor version: 2.5

The package contains functions for exploratory oligonucleotide array analysis. The dependance to tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.

Author: 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

Maintainer: Rafael A. Irizarry

To install this package, start R and enter:

source("http:///biocLite.R")
biocLite("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

Reference Manual

Details

biocViews	Microarray, OneChannel, Preprocessing
Depends	R, Biobase
Imports	affyio, Biobase, graphics, grDevices, methods, preprocessCore, stats, utils
Suggests	tkWidgets, affydata
System Requirements
License	LGPL (>= 2.0)
URL
Depends On Me	adSplit, affyContam, affycoretools, AffyExpress, affylmGUI, affyPara, affypdnn, affyPLM, affyQCReport, AffyTiling, AgiMicroRna, altcdfenvs, arrayMvout, ArrayTools, bgx, dualKS, ecolitk, exonmap, gcrma, GeneTraffic, Harshlight, logitT, lumi, maDB, makecdfenv, panp, plier, plw, puma, qpcrNorm, RefPlus, rHVDM, RPA, simpleaffy, sscore, Starr, webbioc
Imports Me	ArrayExpress, arrayQualityMetrics, ArrayTools, gcrma, HTqPCR, matchprobes, puma, simpleaffy, tilingArray, vsn
Suggests Me	AnnotationDbi, beadarray, beadarraySNP, BiocCaseStudies, Biostrings, BufferedMatrixMethods, factDesign, GeneRegionScan, hexbin, limma, made4, matchprobes, oneChannelGUI, siggenes
Version	1.24.2

Package Downloads

Package Source	affy_1.24.2.tar.gz
Windows Binary	affy_1.24.2.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	affy_1.24.2.tgz
Package Downloads Report	Download Stats