Very simple high level analysis of Affymetrix data

Bioconductor version: 2.10

Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. Makes heavy use of the affy library. Also has some basic scatter plot functions and mechanisms for generating high resolution journal figures...

Author: Crispin J Miller

Maintainer: Crispin Miller <cmiller at>

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



PDF R Script QCandSimpleaffy.pdf
PDF R Script simpleaffy primer
PDF   Reference Manual


biocViews Annotation, Bioinformatics, DataImport, DifferentialExpression, Microarray, OneChannel, Preprocessing, QualityControl, ReportWriting, Software, Transcription, Visualization
Depends R (>= 2.0.0), methods, utils, grDevices, graphics, stats, BiocGenerics(>= 0.1.12), Biobase, affy(>= 1.33.6), genefilter, gcrma
Imports methods, utils, grDevices, graphics, stats, BiocGenerics, Biobase, affy, genefilter, gcrma
System Requirements
License GPL (>= 2)
Depends On Me yaqcaffy
Imports Me affyQCReport, arrayMvout, arrayQualityMetrics
Suggests Me AffyExpress, ArrayTools
Version 2.32.0
Since Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source simpleaffy_2.32.0.tar.gz
Windows Binary (32- & 64-bit)
MacOS 10.5 (Leopard) binary simpleaffy_2.32.0.tgz
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