2.27版本的变化 ----------------------- 阿新特性添加写。AnnotatedDataFrame功能;塞缪尔的请求。granjeaud CHANGES IN VERSION 2.21 ----------------------- USER VISIBLE CHANGES o channelNames<-，NChannelSet，*-methods允许重命名通道o NChannelSet有效性要求所有assayDataElementNames()在varMetadata()$channel中的级别。更新AnnotatedDataFrame不再从部分匹配的列名中复制元数据。2.19版本的变化----------------------- USER VISIBLE CHANGES o dimnames()， rownames()， colnames()和setters工作在eset派生对象上。2.17版本的变化----------------------- USER VISIBLE CHANGES o l2e()，以前弃用，已经失效。o所有在之前发布周期中失效的对象都已被移除。这包括geneNames, getExpData, eList, reporterNames, getBiocRepos, read。expset, updateOldMiame, df2pD, read。pD,阅读。表型数据、exprData、exprList和表型数据。2.11版本中的变化---------------------- USER VISIBLE CHANGES o 'l2e'已不支持，在base中使用'list2env'代替o MIAME类移动到MIAxE虚拟类的子类NEW FEATURES o添加MIAxE虚拟类以保存实验元数据类CHANGES IN VERSION 2.7 ---------------------- USER VISIBLE CHANGES o 'show,eSet-method'汇总协议数据，如果可用。o为SnpSet添加'snpCall' 'snpCallProbability'访问器。 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