xps

Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

The package handles pre-processing, normalization, filtering and analysis of Affymetrix GeneChip expression arrays, including exon arrays (Exon 1.0 ST: core, extended, full probesets), gene arrays (Gene 1.0 ST) and plate arrays on computers with 1 GB RAM only. It imports Affymetrix .CDF, .CLF, .PGF and .CEL as well as annotation files, and computes e.g. RMA, MAS5, FARMS, DFW, MAS5-calls, DABG-calls, I/NI-calls. It is an R wrapper to XPS (eXpression Profiling System), which is based on ROOT, an object-oriented framework developed at CERN. Thus, the prior installation of ROOT is a prerequisite for the usage of this package, however, no knowledge of ROOT is required. ROOT is licensed under LGPL and can be downloaded from http://root.cern.ch.

Author Christian Stratowa, Vienna, Austria

Maintainer Christian Stratowa

To install this package, start R and enter:

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

Documentation

3. XPS Vignette: Comparison APT vs XPS	PDF	R Script
1. XPS Vignette: Overview	PDF	R Script
2. XPS Vignette: Classes	PDF	R Script
Reference Manual

Details

URL
biocViews	ExonArray , GeneExpression , Microarray , OneChannel , DataImport , Preprocessing
Depends	R , methods
Imports
Suggests
System Requirements	root_v5.22.00 <http://root.cern.ch> - See README file for installation instructions.
License	GPL (>= 2.0)
Depends On Me
Imports Me
Suggests Me
Development History	Bioconductor Changelog

Package Downloads

Package source	xps_1.4.10.tar.gz
Windows binary	xps_1.4.10.zip
MacOS X 10.4 (Tiger) binary	Not Available
MacOS X 10.5 (Leopard) binary	xps_1.4.10.tgz
Package Downloads Report	Downloads Stats