
		CHANGES IN R VERSION 3.00.X


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 

