geneChip Analysis Package

Bioconductor version: 2.9

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 <xueli at>

To install this package, start R and enter:


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



PDF R Script 1. Primer
PDF   Reference Manual


biocViews Microarray, OneChannel, QualityControl, Preprocessing, Statistics, DifferentialExpression, Annotation, ReportWriting, Visualization
Depends R (>= 2.7.0), affy(>= 1.23.4), Biobase(>= 2.5.5), methods
Imports affy, Biobase, graphics, grDevices, limma, methods, stats, utils, xtable
Suggests simpleaffy, R2HTML, affydata, affyPLM, genefilter, annaffy, gcrma, hugene10sttranscriptcluster.db
System Requirements
License LGPL (>= 2.0)
Depends On Me
Imports Me
Suggests Me
Version 1.14.0
Since Bioconductor 2.3 (R-2.8)

Package Downloads

Package Source ArrayTools_1.14.0.tar.gz
Windows Binary (32- & 64-bit)
MacOS 10.5 (Leopard) binary ArrayTools_1.14.0.tgz
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