xps

Methods for Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays and Gene Arrays

The package handles pre-processing, normalization, filtering and analysis of Affymetrix GeneChip expression arrays, including exon array systems (Exon 1.0 ST: core, extended, full probesets) and gene array systems (Gene 1.0 ST) 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, 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.

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

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