ArrayTools

geneChip Analysis Package

Bioconductor version: 2.6

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 coh.org>

To install this package, start R and enter:

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

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

    citation("ArrayTools")

Documentation

PDF	R Script	1. Primer
PDF		Reference Manual

Details

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)
URL
Depends On Me
Imports Me
Suggests Me
Version	1.8.0
Since	Bioconductor 2.3 (R-2.8)

Package Downloads

Package Source	ArrayTools_1.8.0.tar.gz
Windows Binary	ArrayTools_1.8.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	ArrayTools_1.8.0.tgz
Package Downloads Report	Download Stats

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