Bioconductor Changelog

Bioconductor Changelog

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ABarray ACME AffyCompatible AffyExpress AnnBuilder AnnotationDbi ArrayExpress BAC BCRANK BGmix BSgenome BioMVCClass Biobase BiocCaseStudies Biostrings BiostringsCinterfaceDemo BufferedMatrix BufferedMatrixMethods CALIB CGHbase CGHcall CGHregions CMA CORREP Category CoCiteStats DEDS DNAcopy DynDoc EBImage EBarrays GEOmetadb GEOquery GGBase GGtools GLAD GOstats GSEABase GSEAlm GeneMeta GeneR GeneRfold GeneSelector GeneSpring GeneTraffic GeneticsBase GeneticsDesign GeneticsPed GenomeGraphs GlobalAncova GraphAT GraphAlignment HELP HEM Harshlight Heatplus Icens KEGGSOAP LBE LMGene LPE LPEadj MANOR MCRestimate MLInterfaces MVCClass MantelCorr MassSpecWavelet MeasurementError.cor MergeMaid Mfuzz MiPP OCplus OLIN OLINgui OrderedList OutlierD PCpheno PGSEA PROcess RBGL RBioinf RLMM RMAGEML ROC RSNPper RWebServices RankProd Ratlpow RbcBook1 Rdbi RdbiPgSQL Rdisop RefPlus Resourcerer Rgraphviz Ringo Rintact Rredland Rtreemix Ruuid SAGx SBMLR SIM SLGI SLqPCR SMAP SNPchip ScISI SemSim ShortRead TypeInfo VanillaICE XDE aCGH adSplit affxparser affy affyPLM affyPara affyQCReport affycomp affycoretools affyio affylmGUI affypdnn altcdfenvs annaffy annotate annotationTools apComplex aroma.light arrayMagic arrayQuality arrayQualityMetrics beadarray beadarraySNP bgafun bgx bioDist biocGraph biocViews biomaRt bridge buildBioC cellHTS cellHTS2 cghMCR clusterStab codelink convert copa cosmo cosmoGUI ctc daMA diffGeneAnalysis ecolitk edd exonmap explorase externalVector factDesign fbat fdrame flowClust flowCore flowQ flowUtils flowViz gaga gaggle gcrma genArise geneRecommender genefilter geneplotter globaltest goCluster goProfiles goTools gpls graph hexbin hopach hypergraph idiogram impute keggorth lapmix limma limmaGUI logicFS lumi maCorrPlot maDB maSigPro maanova macat made4 maigesPack makePlatformDesign makecdfenv marray matchprobes mdqc metaArray multtest ncdfExts nem nnNorm nudge occugene oligo oligoClasses oneChannelGUI ontoTools pairseqsim pamr panp pathRender pcaMethods pcot2 pdInfoBuilder pdmclass pgUtils pickgene pkgDepTools plateCore plgem plier plw ppiStats prada preprocessCore prism puma quantsmooth qvalue rHVDM rama rbsurv reb rflowcyt rhdf5 rsbml rtracklayer safe sagenhaft seqLogo sigPathway siggenes simpleaffy simulatorAPMS sizepower smoothMiner snapCGH snpMatrix spikeLI spkTools splicegear splots spotSegmentation sscore ssize stam stepNorm tilingArray timecourse tkWidgets topGO twilight vbmp vsn weaver webbioc widgetInvoke widgetTools xcms xcmsGUI xps yaqcaffy Subscribe Subscribe to the Bioconductor Changlog.	Fri, 22 Feb 2008 factDesign Changed documentation to reflect that the estrogen data set is an ExpressionSet rather than an exprSet object. [/factDesign] permanent link BioMVCClass Now import class ExpressionSet rather than exprSet from Biobase package to reflect changes in code. [/BioMVCClass] permanent link beadarraySNP Improved handling of chromosome as a factor in featureData for several reports [/beadarraySNP] permanent link bioDist In locf2func, added some infrastructure to automatically increase the maximum number of bins to use in locfit calls in order to support KLD.matrix() calls. In the vignette, cleaned up text body, added a title, and and added section headings. [/bioDist] permanent link makecdfenv Changed exprSet to Cdf when explaining the show method for objects of class Cdf. [/makecdfenv] permanent link clusterStab Updated the class of the fibroEset object from package fibroEset to be ExpressionSet rather than exprSet. [/clusterStab] permanent link plier Updated reference to the return object to reflect it is of class ExpressionSet rather than exprSet. [/plier] permanent link copa Updated class of colonCA data from package colonCA to be ExpressionSet rather than exprSet. [/copa] permanent link Ringo Fixed a typo in the help file title. (Changed exprSet to ExpressionSet since that is what the function returns.) [/Ringo] permanent link sscore Changed an exprSet reference to ExpressionSet to reflect code changes made in SVN revision 23873. [/sscore] permanent link GEOquery Changed references from exprSet to ExpressionSet in the documentation to reflected changes that were made in the code. [/GEOquery] permanent link quantsmooth Use segmented way of smoothing in plotSmoothed() to improve performance [/quantsmooth] permanent link affxparser Last commit contained an embarrassing bug. Fixed Fixed the loading of R.utils in findFiles. This loading had bad consequences for R CMD check - unfortunately. A better fix would be to take care of the problem at its root. [/affxparser] permanent link explorase Permit replicate averaging after analysis. Remember experimental data type when matrix passed via explorase() function. Remove stray browser(). [/explorase] permanent link plw Corrected discussion of rma() function from affy package. It now returns an object of class ExpressionSet rather than exprSet. [/plw] permanent link rHVDM Changed a reference from exprSet to ExpressionSet that was missed when support for ExpressionSet was added. [/rHVDM] permanent link oneChannelGUI Changed exprSet to ExpressionSet in code comments to reflect changes in code. [/oneChannelGUI] permanent link plgem Corrected the object class for LPSeset, which is now an ExpressionSet rather than an exprSet. [/plgem] permanent link xcms Wiki Markup Fixed an off-by-one bug in group.mzClust [/xcms] permanent link ROC Changed code in the vignette to use Biobase's sample.ExpressionSet data object rather than Biobase's eset data object to remove reliance on soon to be defunct exprSet class. [/ROC] permanent link