To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

xps

 

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

Bioconductor version: Release (3.1)

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>

Citation (from within R, enter citation("xps")):

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("xps")

 

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 1.28.0
In Bioconductor since BioC 2.2 (R-2.7) (7 years)
License GPL (>= 2.0)
Depends R (>= 2.6.0), methods, utils
Imports
LinkingTo
Suggests tools
SystemRequirements GNU make, root_v5.34.05 - See README file for installation instructions.
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source xps_1.28.0.tar.gz
Windows Binary xps_1.28.0.zip (32-bit only)
Mac OS X 10.6 (Snow Leopard) xps_1.28.0.tgz
Mac OS X 10.9 (Mavericks) xps_1.28.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/xps/tree/release-3.1
Package Short Url http://bioconductor.org/packages/xps/
Package Downloads Report Download Stats

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