ArrayTools

geneChip Analysis Package

Bioconductor version: Development (2.8)

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:///biocLite.R")
biocLite("ArrayTools")    

Documentation

PDF

R Script

1. Primer

Reference Manual

Details

biocViews	Microarray, OneChannel, QualityControl, Preprocessing, Statistics, DifferentialExpression, Annotation, ReportWriting, Visualization
Depends	R, affy, Biobase, 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)
URL
Depends On Me
Imports Me
Suggests Me
Version	1.11.0

Package Downloads

Package Source	ArrayTools_1.11.0.tar.gz
Windows Binary	ArrayTools_1.11.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	ArrayTools_1.11.0.tgz
Package Downloads Report	Download Stats