xps-package {xps} | R Documentation |
xps Package Overview
Important data classes: SchemeTreeSet
,
DataTreeSet
,
ExprTreeSet
,
CallTreeSet
,
FilterTreeSet
,
AnalysisTreeSet
.
Full help on methods and associated functions is available from
within class help pages.
Additional data classes: ProjectInfo
,
PreFilter
, UniFilter
.
The package handles pre-processing, normalization, filtering and analysis of Affymetrix GeneChip expression arrays, including GeneChip exon array systems (Exon 1.0 ST) and gene array systems (Gene 1.0 ST) on computers with 1-2 GB RAM only. It imports Affymetrix .CDF, .CLF, .PGF and .CEL as well as annotation files, and computes e.g. RMA, MAS5, DABG-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, see the README file. However, no knowledge of ROOT is required. ROOT is licensed under LGPL and can be downloaded from http://root.cern.ch.
Christian Stratowa cstrato@aon.at