xps

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

Bioconductor version: 2.8

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

Details

biocViews ExonArray, GeneExpression, Microarray, OneChannel, DataImport, Preprocessing, Transcription, DifferentialExpression
Depends R (>= 2.6.0), methods
Imports
Suggests
System Requirements root_v5.27.04 - See README file for installation instructions.
License GPL (>= 2.0)
URL
Depends On Me
Imports Me
Suggests Me
Version 1.12.1
Since Bioconductor 2.2 (R-2.7)

Package Downloads

Package Source xps_1.12.1.tar.gz
Windows Binary xps_1.12.1.zip (32-bit only)
MacOS 10.5 (Leopard) binary xps_1.12.1.tgz
Package Downloads Report Download Stats

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