simpleaffy

Very simple high level analysis of Affymetrix data

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://bioconductor.org/biocLite.R")
    biocLite("simpleaffy")

Documentation

QCandSimpleaffy.pdf	PDF
simpleaffy primer	PDF	R Script
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 version 2 or later
URL	http://www.bioconductor.org, http://bioinformatics.picr.man.ac.uk/simpleaffy/
Depends On Me	affyQCReport , yaqcaffy
Imports Me	arrayMvout , arrayQualityMetrics , yaqcaffy
Suggests Me	AffyExpress , ArrayTools
Development History	Bioconductor Changelog

Package Downloads

Package source	simpleaffy_2.20.0.tar.gz
Windows binary	simpleaffy_2.20.0.zip
MacOS X 10.4 (Tiger) binary	simpleaffy_2.20.0.tgz
MacOS X 10.5 (Leopard) binary	simpleaffy_2.20.0.tgz
Package Downloads Report	Downloads Stats