ArrayTools

geneChip Analysis Package

This package is designed to provide solutions for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. The package generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases.

Author	Xiwei Wu, Arthur Li
Maintainer	Arthur Li

To install this package, start R and enter:

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

Documentation

1. Primer	PDF	R Script
Reference Manual

Details

biocViews	Microarray , OneChannel , QualityControl , Preprocessing , Statistics , DifferentialExpression , Annotation , ReportWriting , Visualization
Depends	R , affy , Biobase , graphics , grDevices , limma , methods , stats , utils , xtable
Imports
Suggests	simpleaffy , R2HTML , affydata , affyPLM , genefilter , annaffy , gcrma , hugene10sttranscriptcluster.db
System Requirements
License	LGPL(>= 2.0)
URL
Depends On Me
Imports Me
Suggests Me
Development History	Bioconductor Changelog

Package Downloads

Package source	ArrayTools_1.4.0.tar.gz
Windows binary	ArrayTools_1.4.0.zip
MacOS X 10.4 (Tiger) binary	ArrayTools_1.4.0.tgz
MacOS X 10.5 (Leopard) binary	ArrayTools_1.4.0.tgz
Package Downloads Report	Downloads Stats