CHANGES IN VERSION 2.37 ----------------------- BUG FIXES o '$' completion on eSet and ExpressionSet works in RStudio. CHANGES IN VERSION 2.33 ----------------------- BUG FIXES o exprs<- enforces value with correct dim, dimnames. CHANGES IN VERSION 2.31 ----------------------- NEW FEATURES o tab completion implemented for eSet classes o head and tail.AnnotatedDataFrame methods introduced CHANGES IN VERSION 2.27 ----------------------- NEW FEATURES o Add write.AnnotatedDataFrame function; request of samuel.granjeaud CHANGES IN VERSION 2.21 ----------------------- USER VISIBLE CHANGES o channelNames<-,NChannelSet,*-methods allow re-naming channels o NChannelSet validity requires all assayDataElementNames() to be levels in varMetadata()$channel. BUG FIXES o Updating an AnnotatedDataFrame no longer duplicates metadata from partially matching column names. CHANGES IN VERSION 2.19 ----------------------- USER VISIBLE CHANGES o dimnames(), rownames(), colnames() and setters work on eSet-derived objects CHANGES IN VERSION 2.17 ----------------------- USER VISIBLE CHANGES o l2e(), previously deprecated, has been made defunct. o All objects made defunct in previous release cycles have been removed. This includes geneNames, getExpData, eList, reporterNames, getBiocRepos, read.exprSet, updateOldMiame, df2pD, read.pD, read.phenoData, exprData, exprList, and phenoData. CHANGES IN VERSION 2.11 ---------------------- USER VISIBLE CHANGES o 'l2e' deprecated, use 'list2env' in base instead o MIAME class moved to subclass of MIAxE virtual class NEW FEATURES o Added MIAxE virtual class to hold experiment meta-data classes CHANGES IN VERSION 2.7 ---------------------- USER VISIBLE CHANGES o 'show,eSet-method' summarizes protocolData, if available. o 'snpCall' 'snpCallProbability' accessors added for SnpSet. BUG FIXES o 'selectSome' returns short factors as character() CHANGES IN VERSION 2.5 ---------------------- USER VISIBLE CHANGES o 'protocolData' slot added to eSet class to store protocol metadata stored in microarray data files; can be accessed by protocolData and set by protocolData<-. o 'sampleNames,NChannelSet-method' returns a vector when the sample names of each channel are the same. CHANGES IN VERSION 2.1 ---------------------- NEW FEATURES o 'makeDataPacakge' method for ExpressionSet now accepts a 'description' argument for the generated manual page. BUG FIXES o combine,matrix,matrix-method would record 'NA' for entries in the second matrix with niether rows nor columns present in the first. o openPDF now checks for NULL or zero-length pdfviewer option CHANGES IN VERSION 2.0 ---------------------- SIGNIFICANT USER-VISIBLE CHANGES o 'combine' on data.frame columns with mismatched levels causes a warning, rather than error. o updateObject does not warn about duplicating locked environment, unlesss verbose=TRUE NEW FEATURES o 'combine' now works to combine rows of ExpressionSet BUG FIXES o AnnotatedDataFrame 'show' listed additional varMetadata column names incorrectly when labelDescription was not the first. NEWLY DEFUNCT CLASSES, METHODS, FUNCTIONS, DATA SETS o Defunct S4 Classes 1) annotatedDataset - class definition still exits to support phenoData conversion 2) exprMatrix - removed class definition 3) exprSet - class definition still exists to allow conversion to ExpressionSet 4) phenoData - class definition still exists to allow conversion to AnnotatedDataFrame o Defunct Generics/Methods 1) addVarMetadataEntry - S4 generic definition removed 2) as.data.frame.exprSet - S3 method removed 3) convertVarLabels - S4 generic definition removed 4) eList - S4 methods remain with .Defunct messages 5) "eList<-" - S4 methods remain with .Defunct messages 6) exprs2excel - S4 generic definition removed 7) getExpData - S4 methods remain with .Defunct messages 8) geneNames - S4 methods remain with .Defunct messages 9) "geneNames<-" - S4 methods remain with .Defunct messages 10) getUnits - S4 generic definition removed 11) getVarMetadata - S4 generic definition removed 12) iter - S4 generic definition removed 13) reporterInfo - S4 generic definition removed 14) "reporterInfo<-" - S4 generic definition removed 15) reporterNames - S4 methods remain with .Defunct messages 16) "reporterNames<-" - S4 methods remain with .Defunct messages 17) split (for use with exprSet objects) - S4 generic definition removed 18) update2MIAME - S4 generic definition removed o Defunct functions 1) df2pD - function stub with .Defunct message 2) read.exprSet - function stub with .Defunct message 3) read.pD - function stub with .Defunct message 4) read.phenoData - function stub with .Defunct message 5) updateOldMiame - function stub with .Defunct message o Defunct data sets 1) bbsym 2) eset - use sample.ExpressionSet instead 3) golubMergeSub 4) sample.eSet - use sample.MultiSet instead 4) sample.exprSet.1 - use sample.ExpressionSet instead 5) sample.exprSet - use sample.ExpressionSet instead 6) SWPD 7) swrep