simpleaffy

Very simple high level analysis of Affymetrix data

Bioconductor version: 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 <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

Details

biocViews Microarray, OneChannel, QualityControl, Preprocessing, Transcription, DataImport, Bioinformatics, DifferentialExpression, Annotation, ReportWriting, Visualization
Depends R (>= 2.0.0), 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 2.28.0
Since Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source simpleaffy_2.28.0.tar.gz
Windows Binary simpleaffy_2.28.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary simpleaffy_2.28.0.tgz
Package Downloads Report Download Stats

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