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

Bioconductor version: Release (3.2)

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

Author: Christian Stratowa, Vienna, Austria

Maintainer: Christian Stratowa <cstrato at>

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


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


biocViews DataImport, DifferentialExpression, ExonArray, GeneExpression, Microarray, OneChannel, Preprocessing, Software, Transcription
Version 1.30.0
In Bioconductor since BioC 2.2 (R-2.7) (7.5 years)
License GPL (>= 2.0)
Depends R (>= 2.6.0), methods, utils
Suggests tools
SystemRequirements GNU make, root_v5.34.05 - See README file for installation instructions.
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