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 DFP 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 HilbertCurveDisplay ITALICS 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 RpsiXML 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 dualKS ecolitk edd exonmap explorase externalVector factDesign fbat fdrame flowClust flowCore flowDB flowQ flowUtils flowViz gaga gaggle gcrma genArise geneRecommender genefilter geneplotter globaltest goCluster goProfiles goTools gpls graph hexbin hopach hypergraph idiogram impute iterativeBMA iterativeBMAsurv keggorth lapmix limma limmaGUI logicFS lumi maCorrPlot maDB maSigPro maanova macat made4 maigesPack makePlatformDesign makecdfenv marray matchprobes mdqc metaArray miRNApath minet multiscan 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.	Wed, 05 Mar 2008 beadarray Replaced usage of defunct reporterInfo and "reporterInfo<-" methods with fData and "fData<-". [/beadarray] permanent link matchprobes Replaced usage of newly defunct class phenoData with AnnotatedDataFrame. [/matchprobes] permanent link rsbml Import/export SBase fields for Models. Also avoid conflict with R macro SET_ATTR (changed to SET_XML_ATTR). Add missing documentation. Also make Model inherit from SBase and add convenience methods for setting dates using POSIXt objects. [/rsbml] permanent link beadarraySNP Replaced usage of defunct reporterInfo and "reporterInfo<-" methods with fData and "fData<-". [/beadarraySNP] permanent link RMAGEML Removed comment containing newly defunct class phenoData. [/RMAGEML] permanent link edd Replaced usage of newly defunct phenoData class with AnnotatedDataFrame. [/edd] permanent link gcrma Replaced usage of newly defunct class phenoData with AnnotatedDataFrame. [/gcrma] permanent link macat Replaced usage of newly defunct phenoData class and geneName method with AnnotatedDataFrame and featureName respectively. [/macat] permanent link Mfuzz Updated the yeast data set from defunct class exprSet to ExpressionSet. [/Mfuzz] permanent link vsn Replaced usage of newly defunct class phenoData with AnnotatedDataFrame. [/vsn] permanent link affxparser Version; 1.11.6 [2008-03-04] o Add ability to parse PGF and CLF files [/affxparser] permanent link oneChannelGUI Added a routine to load ILLUMINA arrays starting from BeadStudio v.1 and 2 output. [/oneChannelGUI] permanent link pdmclass Replaced usage of defunct method geneName with featureName in vignette. Also quoted the component arguments to model.extract calls to conform with standard usage. [/pdmclass] permanent link lumi Removed commented out code that references newly defunct class phenoData. [/lumi] permanent link Category Replace the usage of now defunct phenoData class with AnnotatedDataFrame. [/Category] permanent link SNPchip corrected mistake in DESCRIPTION [/SNPchip] permanent link simpleaffy Replaced usage of newly defunct class phenoData with AnnotatedDataFrame. [/simpleaffy] permanent link metaArray Replaced usage of defunct phenoData class with AnnotatedDataFrame in vignette. [/metaArray] permanent link Biobase Fixed a typo in the featureData help file. Provide more informative messages when calling validity methods for classes exprSet and phenoData. [/Biobase] permanent link