simpleaffy

Very simple high level analysis of Affymetrix data

Bioconductor version: Development (2.8)

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

To install this package, start R and enter:

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

Documentation

PDF QCandSimpleaffy.pdf
PDF R Script simpleaffy primer

Reference Manual

Details

biocViews Microarray, OneChannel, QualityControl, Preprocessing, Transcription, DataImport, Bioinformatics, DifferentialExpression, Annotation, ReportWriting, Visualization
Depends R, affy, genefilter, Biobase, methods, utils, gcrma
Imports affy, Biobase, gcrma, genefilter, graphics, grDevices, methods, stats, utils
Suggests
System Requirements
License GPL (>= 2)
URL http://www.bioconductor.org, http://bioinformatics.picr.man.ac.uk/simpleaffy/
Depends On Me yaqcaffy
Imports Me affyQCReport, arrayMvout, arrayQualityMetrics
Suggests Me AffyExpress, ArrayTools
Version 2.27.1

Package Downloads

Package Source simpleaffy_2.27.1.tar.gz
Windows Binary simpleaffy_2.27.1.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary simpleaffy_2.27.1.tgz
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