xps

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

Bioconductor version: Development (3.0)

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, FIRMA, tRMA, 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 <cstrato at aon.at>

To install this package, start R and enter:

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

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

    citation("xps")

Documentation

PDF R Script 1. XPS Vignette: Overview
PDF R Script 2. XPS Vignette: Classes
PDF R Script 3. XPS Vignette: Comparison APT vs XPS
PDF R Script 4. XPS Vignette: Function express()
PDF   Reference Manual
Text   README
Text   NEWS

Details

biocViews DataImport, DifferentialExpression, ExonArray, GeneExpression, Microarray, OneChannel, Preprocessing, Software, Transcription
Version 1.25.0
In Bioconductor since BioC 2.2 (R-2.7)
License GPL (>= 2.0)
Depends R (>= 2.6.0), methods, utils
Imports
Suggests tools
System Requirements root_v5.34.05 - See README file for installation instructions.
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source xps_1.25.0.tar.gz
Windows Binary xps_1.25.0.zip (32-bit only)
Mac OS X 10.6 (Snow Leopard) xps_1.25.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center