xps-package {xps} | R Documentation

## xps Package Overview

### Description

xps Package Overview

### Details

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 exon array systems (Exon 1.0 ST: core, extended, full probesets), gene array systems (Gene 1.0 ST) and plate array systems 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 http://root.cern.ch.

### Author(s)

Christian Stratowa cstrato@aon.at

[Package xps version 1.4.10 Index]