simpleaffy

Very simple high level analysis of Affymetrix data

Bioconductor version: Release (2.12)

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 picr.man.ac.uk>

To install this package, start R and enter:

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

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

    citation("simpleaffy")

Documentation

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

Details

biocViews Annotation, Bioinformatics, DataImport, DifferentialExpression, Microarray, OneChannel, Preprocessing, QualityControl, ReportWriting, Software, Transcription, Visualization
Version 2.36.1
In Bioconductor since BioC 1.6 (R-1.11) 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
Suggests
System Requirements
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

Package Downloads

Package Source simpleaffy_2.36.1.tar.gz
Windows Binary simpleaffy_2.36.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) simpleaffy_2.36.1.tgz
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