\HeaderA{xps-package}{xps Package Overview}{xps.Rdash.package}
\aliasA{xps}{xps-package}{xps}
\keyword{package}{xps-package}
\begin{Description}\relax
xps Package Overview
\end{Description}
\begin{Details}\relax
Important data classes: \code{\LinkA{SchemeTreeSet}{SchemeTreeSet}},
\code{\LinkA{DataTreeSet}{DataTreeSet}},
\code{\LinkA{ExprTreeSet}{ExprTreeSet}},
\code{\LinkA{CallTreeSet}{CallTreeSet}},
\code{\LinkA{FilterTreeSet}{FilterTreeSet}},
\code{\LinkA{AnalysisTreeSet}{AnalysisTreeSet}}.
Full help on methods and associated functions is available from
within class help pages.

Additional data classes: \code{\LinkA{ProjectInfo}{ProjectInfo}},
\code{\LinkA{PreFilter}{PreFilter}}, \code{\LinkA{UniFilter}{UniFilter}}.

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 Affymetrix 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, see the README file. However, no knowledge of ROOT
is required. ROOT is licensed under LGPL and can be downloaded from \url{http://root.cern.ch}.
\end{Details}
\begin{Author}\relax
Christian Stratowa \email{cstrato@aon.at}
\end{Author}

