Bioconductor-mirror/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, 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

Getting started

Package details

AuthorChristian Stratowa, Vienna, Austria
Bioconductor views DataImport DifferentialExpression ExonArray GeneExpression Microarray OneChannel Preprocessing Transcription
MaintainerChristian Stratowa <[email protected]>
LicenseGPL (>= 2.0)
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
Bioconductor-mirror/xps documentation built on June 1, 2017, 8:13 p.m.