Very simple high level analysis of Affymetrix data

Bioconductor version: Release (2.11)

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>

To install this package, start R and enter:


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



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


biocViews Annotation, Bioinformatics, DataImport, DifferentialExpression, Microarray, OneChannel, Preprocessing, QualityControl, ReportWriting, Software, Transcription, Visualization
Version 2.34.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier
License GPL (>= 2)
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
Depends On Me yaqcaffy
Imports Me affyQCReport, arrayMvout, arrayQualityMetrics
Suggests Me AffyExpress, ArrayTools

Package Downloads

Package Source simpleaffy_2.34.0.tar.gz
Windows Binary (32- & 64-bit)
MacOS 10.5 (Leopard) simpleaffy_2.34.0.tgz
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