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
