Package: xps
Version: 1.22.2
Title: Processing and Analysis of Affymetrix Oligonucleotide Arrays
        including Exon Arrays, Whole Genome Arrays and Plate Arrays
Author: Christian Stratowa, Vienna, Austria
Maintainer: Christian Stratowa <cstrato@aon.at>
Depends: R (>= 2.6.0), methods, utils
Suggests: tools
Description: 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 http://root.cern.ch.
License: GPL (>= 2.0)
Collate: utils.R TreeSetClasses.R methods.ProjectInfo.R
        methods.Filter.R methods.PreFilter.R methods.UniFilter.R
        methods.TreeSet.R methods.SchemeTreeSet.R methods.ProcesSet.R
        methods.DataTreeSet.R methods.ExprTreeSet.R
        methods.CallTreeSet.R methods.QualTreeSet.R
        methods.FilterTreeSet.R methods.AnalysisTreeSet.R
        Constructors.R import.R export.R root.files.R rma.R mas4.R
        mas5.R mas5.call.R dabg.call.R dfw.R farms.R ini.call.R firma.R
        trma.R bgcorrect.R normalize.R summarize.R express.R fitQC.R
        qualify.R AffyRNAdeg.R filter.R plot.R root.graphics.R
        xpsQAReport.R zzz.R
biocViews: ExonArray, GeneExpression, Microarray, OneChannel,
        DataImport, Preprocessing, Transcription,
        DifferentialExpression
LazyLoad: yes
SystemRequirements: root_v5.34.05 <http://root.cern.ch> - See README
        file for installation instructions.
Packaged: 2013-12-22 07:52:47 UTC; biocbuild
Built: R 3.0.2; i386-w64-mingw32; 2013-12-22 16:14:56 UTC; windows
Archs: i386
