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