CHANGES IN R VERSION 3.2.X VERSION xps-1.29.1 o update README file VERSION xps-1.27.1 o add SystemRequirements GNU make CHANGES IN R VERSION 3.1.X VERSION xps-1.25.2 o update XPSPreProcessing.cxx to reset mask to initial values for each array (necessary for whole genome/exon arrays) VERSION xps-1.25.1 o update XPSPreProcessing.cxx to remove -Wsequence-point warning for numsels = ++numsels CHANGES IN R VERSION 3.00.X VERSION xps-1.23.2 o add type CNRTYPE to image() and hist() VERSION xps-1.21.5 o add QualTreeSet methods NUSE() and RLE() to get stats and values o update man export.Rd VERSION xps-1.21.4 o update xpsQAReport.R for R-3.x VERSION xps-1.21.3 o update XPSSchemes.cxx to replace error with warning for missing annotation header '%netaffx-annotation-' VERSION xps-1.21.2 o update XPSNormalizer.cxx to correct for uninitialized variables VERSION xps-1.21.1 o update README o update Makefile to set include path (for ~/.R/Makevars) o update XPSUtils.cxx to eliminate warning with clang VERSION xps-1.19.10 o update XPSSchemes.cxx to correct possible memory error in TString array names[i] VERSION xps-1.19.9 o update README VERSION xps-1.19.8 o replace .path.package() with path.package() VERSION xps-1.19.7 o update XPSSchemes.cxx to replace error with warning for missing annotation header '%genome-species' VERSION xps-1.19.2 - 6 o update configure.win and Makefile.win for ROOT compiled with MinGW; xps works now on Windows 7 VERSION xps-1.19.1 o update Import..Annotation() methods in XPSchemes.cxx to protect against tabs in Affymetrix annotation files o update script4schemes.R to include schemes with annotation na33 CHANGES IN R VERSION 2.15.X VERSION xps-1.17.2 o update script4schemes.R to include schemes for HuGene-2_x-st arrays o update script4xps.R with example 4a for HuGene-2_1-st arrays o update README VERSION xps-1.17.1 o remove warnings: partial argument match o zzz.R: use .onAttach() VERSION xps-1.15.2 o move to ROOT version 5.32/01, update README VERSION xps-1.15.1 o update zzz.R CHANGES IN R VERSION 2.14.0 VERSION xps-1.13.10 o update function xpsQAReport() to replace "_" with "\_" for *.Rnw VERSION xps-1.13.9 o add quality report function xpsQAReport() o update vignette xps.Rnw VERSION xps-1.13.8 o add functions attachProbe(), removeProbe(), etc. o add functions contentGC(), probeSequence() o add functions inten2GCplot(), plotInten2GC() o update vignette xps.Rnw VERSION xps-1.13.7 o add function unitID2symbol() o add function plotProbeset() o update vignette xps.Rnw VERSION xps-1.13.6 o update function indexUnits() for exon probesets o add function symbol2unitID() o add function probesetplot() VERSION xps-1.13.5 o update script4schemes.R to include schemes with annotation na32 o update script4xps.R and script4exon.R VERSION xps-1.13.4 o move to ROOT version 5.30/00, update README o update vignettes xps.Rnw and xpsClasses.Rnw VERSION xps-1.13.3 o correct problem in unitID2affyID() on Linux caused by sQuote() VERSION xps-1.13.2 o add functions plotXXX() o function hist() no longer requires to attachInten() o add functions indexUnits(), pmindex(), mmindex() o add functions probesetID2unitID(), unitID2probesetID(), etc o add functions attachUnitNames(), removeUnitNames() o add functions attachDataXY(), removeDataXY() VERSION xps-1.13.1 o update function plotImage() to draw background images CHANGES IN R VERSION 2.13.0 VERSION xps-1.11.12 o update functions: plotBoxplot(), plotAffyRNAdeg() VERSION xps-1.11.11 o update functions: plotImage(), plotAffyRNAdeg() VERSION xps-1.11.10 o add functions: plotImage(), plotBoxplot() o update methods image() VERSION xps-1.11.9 o add method: pcaplot() o update method plotAffyRNAdeg() VERSION xps-1.11.8 o add methods: corplot(), madplot() VERSION xps-1.11.7 o update method plotAffyRNAdeg() VERSION xps-1.11.6 o add methods for RNA degradation plots: xpsRNAdeg(), plotAffyRNAdeg() o add man pages VERSION xps-1.11.5 o correct minor bug in XPSProcessing.cxx: ExportExprTreeInfo() o update method image() o add man pages VERSION xps-1.11.4 o add new class QualTreeSet to add quality control features o add functions qualify() and fitQC() and derived functions o add method image() for residual plots of IVT, Gene ST, Exon ST and plate arrays o add new plots coiplot() and borderplot() o update boxplot(), callplot(), image() to be independent of slot 'data' VERSION xps-1.11.3 o add function trma() VERSION xps-1.11.1 o update DESCRIPTION to correct SystemRequirements to root_v5.27.04 o update function READ_WSTRING() to handle big endian for PPC CHANGES IN R VERSION 2.12.0 VERSION xps-1.9.9 o update method XExonChip::ProbesetLevel() for whole genome annotation na31 files VERSION xps-1.9.8 o revert update of Makefile.win VERSION xps-1.9.7 o update Makefile.win to clean xpsLinkDef.h o update script4schemes.R for annotation na31 (updated release) VERSION xps-1.9.6 o update information files for new ROOT Version 5.27/04 (root_v5.27/04) o update script4xps.R, script4schemes.R for annotation na31 VERSION xps-1.9.5 o update import.data to use make.names(celnames) to protect against certain characters VERSION xps-1.9.4 o update root.profile.R, macroDrawProfilePlot.C to allow selecting subset of trees o in read.table() set stringsAsFactors=FALSE VERSION xps-1.9.3 o update method XPreFilter::Calculate() to handle exon arrays correctly VERSION xps-1.9.2 o update Makefile and Makefile.arch VERSION xps-1.9.1 o add support in XPSAnalysis.cxx to export exon array probeset annotations (filters) CHANGES IN R VERSION 2.11.0 VERSION xps-1.7.9 o update method validData() to handle slot data containing different column types o update methods seExprTreeSet(), rleplot(), mvaplot(), nuseplot() VERSION xps-1.7.8 o add method xpsFIRMA() o add functions firma(), firma.expr(), firma.score() VERSION xps-1.7.7 o update bgcorrect.R to warn from using tmpdir resulting in empty root file o update normalize.R to warn from using tmpdir resulting in empty root file VERSION xps-1.7.6 o minor change to allow computation with g++ 4.4.x VERSION xps-1.7.4 o add NEWS VERSION xps-1.7.3 o add ExprTreeSet methods validSE(), nuseplot(), rleplot() o allow to export layout trees for incomplete *.CLF files o update examples/updateAnnotation.R VERSION xps-1.7.2 o add examples/updateAnnotation.R o update script4xps.R VERSION xps-1.7.1 o allow using mas5() and mas5.call() with plate arrays w/o MMs o update script4xps.R CHANGES IN R VERSION 2.10.0 VERSION xps-1.5.19 o update script4xps.R VERSION xps-1.5.18 o add parameter bgcorrect.option to function mas5.call() VERSION xps-1.5.17 o update README VERSION xps-1.5.16 o allow handling of probesets w/o MMs on Citrus.CDF VERSION xps-1.5.15 o validBgrd() implement 'which' o add vignette xpsPreprocess.pdf o add example/macro4xpsPreprocess.R VERSION xps-1.5.14 o update export() to include read.table(..,comment.char='') o update methods.DataTreeSet.R to allow probe-level lowess and supsmu normalization VERSION xps-1.5.13 o update express() to allow setting bufsize for tree baskets VERSION xps-1.5.12 o changes to allow import of miRNA-1_0.CDF VERSION xps-1.5.9 o update validOption() to allow 'separate:none' VERSION xps-1.5.8 o update rma() to allow improved ties handling as option like preprocessCore VERSION xps-1.5.7 o update method validCall() o add methods validExpr() and validPVal() o update vignette APTvsXPS.pdf o update examples script4xps2apt.R and script4bestmatch.R VERSION xps-1.5.4 o update function exonLevel() to use affx=c(4,8,16,32) o update function dataDataTreeSet() to return correct ids for mask o add new internal function exonLevelIDs() VERSION xps-1.5.3 o update help file exonLevel.Rd VERSION xps-1.5.1 o update validData() to check for duplicate rownames o allow reading of genetitan plate data CHANGES IN R VERSION 2.9.0 VERSION xps-1.3.13 o update DESCRIPTION to mention root version o update README VERSION xps-1.3.12 o correct bug in implementation of FDR and Hochberg VERSION xps-1.3.11 o make function exonLevel public and add exonLevel.Rd VERSION xps-1.3.8 o update all initialize methods to prevent checkS3forClass warnings o update bgcorrect.rma, bgcorrect.mas5 o update script4xps.R, script4exon.R VERSION xps-1.3.6 o support using genome array as exon arrays VERSION xps-1.3.5 o add code in function import.data() to replace dots, colons in celnames with underscores VERSION xps-1.3.4 o correct bug in xpsPreprocess for add.data=FALSE o correct sub(.root, .txt, x) to sub(\.root, .txt, x) o update root.image() to get setname from setName() VERSION xps-1.3.3 o change intensity<- to allow using slot data for further processing VERSION xps-1.3.1 o add function root.merge.data() CHANGES IN R VERSION 2.8.0 VERSION xps-1.1.9 o protect class XRMABackground against defect Affy chips, e.g. zero division o protect root.data() etc against duplicate celnames or treenames VERSION xps-1.1.8 o correct bug in class XINICall resulting in buffer overflow VERSION xps-1.1.7 o add call method I/NI-call (Talloen et al) VERSION xps-1.1.6 o prevent import of CEL-files with zero max intensity o update functions returning ExprTreeSet to import results as option only o update functions returning CallTreeSet to import results as option only o update root.density etc to allow saving from R function o add root.profile to use root graphics for boxplots o add summarization method FARMS (Hochreiter et al) o add summarization method DFW (Chen et al) o update vignette xps.pdf VERSION xps-1.1.5 o correct problem in validData for CEL-files starting with numbers VERSION xps-1.1.4 o update vignette xps.pdf o add new vignette APTvsXPS.pdf o update examples script4exon.R o add examples script4xps2apt.R and script4bestmatch.R o update README VERSION xps-1.1.3 o to allow CEL-names starting with a number, update to read.table(..., check.names=FALSE) o update ExprTreeSet to set slot exprtype to correct type o add functions root.expr() and root.call() o need to change setname for dabg.call() from CallTreeSet to CallSet as for mas5.call() VERSION xps-1.1.2 o allow different exonlevels for bgrd, normalization, summarization o update replacement methods exprs, pvalData, presCall to allow subsetting o add function metaProbesets to compute metacoreList.mps for apt VERSION xps-1.1.1 o increase maximum root file size from 2GB to 2TB o decrease computation time o correct bug preventing export of exon probeset normalized data CHANGES IN R VERSION 2.7.0 VERSION xps-0.99.11 o correct bug resulting in empty exon probeset column VERSION xps-0.99.10 o update source code to handle tmpdir correctly on WinXP o update examples script4xps.R and script4exon.R VERSION xps-0.99.9 o update methods namePart, extenPart, validData, validBgrd to handle names with underscores VERSION xps-0.99.8 o update functions root.xxx to work with WinXP VERSION xps-0.99.3 o package can now be built for Windows XP o added possibility to add current date and/or time to root filename o added function existsROOTFile o updated vignette xps.Snw VERSION xps-0.4.3 o new method rawCELName() to get the names of the imported CEL-files VERSION xps-0.4.2 o add support to import generic (calvin) CEL-files o update method volcanoplot VERSION xps-0.4.1 o change DESCRIPTION o add method volcanoplot o correct update bug in xpsUniFilter VERSION xps-0.4.0 o import.data: import CEL-files from different directories o update DESCRIPTION, NAMESPACE o add possibility to apply non-sepcific filters and univariate filters o add S4 classes Filter, PreFilter, UniFilter o add S4 classes FilterTreeSet and AnalysisTreeSet