simpleaffy

Very simple high level analysis of Affymetrix data

Bioconductor version: 2.6

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	affyQCReport, yaqcaffy
Imports Me	arrayMvout, arrayQualityMetrics, yaqcaffy
Suggests Me	AffyExpress, ArrayTools
Version	2.24.0
Since	Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source	simpleaffy_2.24.0.tar.gz
Windows Binary	simpleaffy_2.24.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	simpleaffy_2.24.0.tgz
Package Downloads Report	Download Stats

Workflows »

Common Bioconductor workflows include:

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Hosting provided by Fred Hutchinson Cancer Research Center