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Very simple high level analysis of Affymetrix data

Bioconductor version: 2.14

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>

Citation (from within R, enter citation("simpleaffy")):


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PDF R Script simpleaffy primer
PDF   Reference Manual


biocViews Annotation, DataImport, DifferentialExpression, Microarray, OneChannel, Preprocessing, QualityControl, ReportWriting, Software, Transcription, Visualization
Version 2.40.0
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
Suggests Me AffyExpress, ArrayTools, ELBOW

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