r-bioc-biobase 2.20.0-1build1 / usr / lib / R / site-library / Biobase / NEWS

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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

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