CHANGES IN VERSION 1.41 ----------------------- o update NEWS file CHANGES IN VERSION 1.39 ----------------------- o XPSData.h - correct selassignment CHANGES IN VERSION 1.37 ----------------------- o configure.in file - unix line endings o update INSTALL and README file CHANGES IN VERSION 1.35 ----------------------- o eliminate dependency on ROOTSYS o update configure.in file o update Makefile.arch to add ROOTSYS an update -rpath o eliminate dependency on DYLD_LIBRARY_PATH and LD_LIBRARY_PATH o update configure.in file o update Makefile.arch to use -rpath with ld o update Makefile for MacOS Sierra o update README file o update import in NAMESPACE CHANGES IN VERSION 1.29 ----------------------- o update README file CHANGES IN VERSION 1.27 ----------------------- o add SystemRequirements GNU make CHANGES IN VERSION 1.25 ----------------------- o update XPSPreProcessing.cxx to reset mask to initial values for each array (necessary for whole genome/exon arrays) o update XPSPreProcessing.cxx to remove -Wsequence-point warning for numsels = ++numsels CHANGES IN VERSION 1.23 ----------------------- o add type CNRTYPE to image() and hist() CHANGES IN VERSION 1.21 ----------------------- o add QualTreeSet methods NUSE() and RLE() to get stats and values o update man export.Rd o update xpsQAReport.R for R-3.x o update XPSSchemes.cxx to replace error with warning for missing annotation header '%netaffx-annotation-' o update XPSNormalizer.cxx to correct for uninitialized variables o update README o update Makefile to set include path (for ~/.R/Makevars) o update XPSUtils.cxx to eliminate warning with clang CHANGES IN VERSION 1.19 ----------------------- o update XPSSchemes.cxx to correct possible memory error in TString array names[i] o update README o replace .path.package() with path.package() o update XPSSchemes.cxx to replace error with warning for missing annotation header '%genome-species' o update configure.win and Makefile.win for ROOT compiled with MinGW; xps works now on Windows 7 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 VERSION 1.17 ----------------------- 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 o remove warnings: partial argument match o zzz.R: use .onAttach() CHANGES IN VERSION 1.15 ----------------------- o move to ROOT CHANGES IN VERSION 5.32/01, update README o update zzz.R CHANGES IN VERSION 1.13 ----------------------- o update function xpsQAReport() to replace "_" with "\_" for *.Rnw o add quality report function xpsQAReport() o update vignette xps.Rnw o add functions attachProbe(), removeProbe(), etc. o add functions contentGC(), probeSequence() o add functions inten2GCplot(), plotInten2GC() o update vignette xps.Rnw o add function unitID2symbol() o add function plotProbeset() o update vignette xps.Rnw o update function indexUnits() for exon probesets o add function symbol2unitID() o add function probesetplot() o update script4schemes.R to include schemes with annotation na32 o update script4xps.R and script4exon.R o move to ROOT CHANGES IN VERSION 5.30/00, update README o update vignettes xps.Rnw and xpsClasses.Rnw o correct problem in unitID2affyID() on Linux caused by sQuote() 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() o update function plotImage() to draw background images CHANGES IN VERSION 1.11 ----------------------- o update functions: plotBoxplot(), plotAffyRNAdeg() o update functions: plotImage(), plotAffyRNAdeg() o add functions: plotImage(), plotBoxplot() o update methods image() o add method: pcaplot() o update method plotAffyRNAdeg() o add methods: corplot(), madplot() o update method plotAffyRNAdeg() o add methods for RNA degradation plots: xpsRNAdeg(), plotAffyRNAdeg() o add man pages o correct minor bug in XPSProcessing.cxx: ExportExprTreeInfo() o update method image() o add man pages 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' o add function trma() o update DESCRIPTION to correct SystemRequirements to root_v5.27.04 o update function READ_WSTRING() to handle big endian for PPC CHANGES IN VERSION 1.9 ---------------------- o update method XExonChip::ProbesetLevel() for whole genome annotation na31 files o revert update of Makefile.win o update Makefile.win to clean xpsLinkDef.h o update script4schemes.R for annotation na31 (updated release) o update information files for new ROOT CHANGES IN VERSION 5.27/04 (root_v5.27/04) o update script4xps.R, script4schemes.R for annotation na31 o update import.data to use make.names(celnames) to protect against certain characters o update root.profile.R, macroDrawProfilePlot.C to allow selecting subset of trees o in read.table() set stringsAsFactors=FALSE o update method XPreFilter::Calculate() to handle exon arrays correctly o update Makefile and Makefile.arch o add support in XPSAnalysis.cxx to export exon array probeset annotations (filters) CHANGES IN VERSION 1.7 ---------------------- o update method validData() to handle slot data containing different column types o update methods seExprTreeSet(), rleplot(), mvaplot(), nuseplot() o add method xpsFIRMA() o add functions firma(), firma.expr(), firma.score() 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 o minor change to allow computation with g++ 4.4.x o add NEWS o add ExprTreeSet methods validSE(), nuseplot(), rleplot() o allow to export layout trees for incomplete *.CLF files o update examples/updateAnnotation.R o add examples/updateAnnotation.R o update script4xps.R o allow using mas5() and mas5.call() with plate arrays w/o MMs o update script4xps.R CHANGES IN VERSION 1.5 ---------------------- o update script4xps.R o add parameter bgcorrect.option to function mas5.call() o update README o allow handling of probesets w/o MMs on Citrus.CDF o validBgrd() implement 'which' o add vignette xpsPreprocess.pdf o add example/macro4xpsPreprocess.R o update export() to include read.table(..,comment.char='') o update methods.DataTreeSet.R to allow probe-level lowess and supsmu normalization o update express() to allow setting bufsize for tree baskets o changes to allow import of miRNA-1_0.CDF o update validOption() to allow 'separate:none' o update rma() to allow improved ties handling as option like preprocessCore o update method validCall() o add methods validExpr() and validPVal() o update vignette APTvsXPS.pdf o update examples script4xps2apt.R and script4bestmatch.R 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() o update help file exonLevel.Rd o update validData() to check for duplicate rownames o allow reading of genetitan plate data CHANGES IN VERSION 1.3.13 ---------------------- o update DESCRIPTION to mention root CHANGES IN VERSION o update README o correct bug in implementation of FDR and Hochberg o make function exonLevel public and add exonLevel.Rd o update all initialize methods to prevent checkS3forClass warnings o update bgcorrect.rma, bgcorrect.mas5 o update script4xps.R, script4exon.R o support using genome array as exon arrays o add code in function import.data() to replace dots, colons in celnames with underscores 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() o change intensity<- to allow using slot data for further processing o add function root.merge.data() o protect class XRMABackground against defect Affy chips, e.g. zero division o protect root.data() etc against duplicate celnames or treenames CHANGES IN VERSION 1.1 ---------------------- o correct bug in class XINICall resulting in buffer overflow o add call method I/NI-call (Talloen et al) 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 o correct problem in validData for CEL-files starting with numbers 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 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() 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 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 VERSION 0.99 ----------------------- o correct bug resulting in empty exon probeset column o update source code to handle tmpdir correctly on WinXP o update examples script4xps.R and script4exon.R o update methods namePart, extenPart, validData, validBgrd to handle names with underscores o update functions root.xxx to work with WinXP 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 CHANGES IN VERSION 0.4 ---------------------- o new method rawCELName() to get the names of the imported CEL-files o add support to import generic (calvin) CEL-files o update method volcanoplot o change DESCRIPTION o add method volcanoplot o correct update bug in xpsUniFilter 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