[Bioc-devel] Refactored Biobase in BioC 2.2 - exprSet and phenoData classes defunct, use ExpressionSet and AnnotatedDataFrame

[Patrick Aboyoun]

I am pleased to announce that the Biobase package has been refactored in 
the BioC 2.2 code line to remove long deprecated classes and methods. 
This cleaner Biobase package will make it easier for new and existing 
users to manage and analyze their data using the best practices within 
the BioConductor community. The main user facing change to Biobase is 
the removal of the long deprecated exprSet and phenoData classes in 
favor of the superior ExpressionSet and AnnotatedDataFrame classes.

Given the scope of the refactoring endeavor, I anticipate it may take a 
little time to stabilize the BioC 2.2 builds. I made modifications to 
some packages within the BioC 2.2 code line to update them from the 
deprecated (exprSet, phenoData) paradigm to the (ExpressionSet, 
AnnotatedDataFrame) paradigm. However, I anticipate a number of BioC 2.2 
package will fail to build and pass check because they still rely on 
exprSet and phenoData objects. If you are a maintainer of one of these 
packages using exprSet & phenoData, please update them to use 
ExpressionSet & AnnotatedDataFrame. Failure to update your package by 14 
April 2008 (see http://wiki.fhcrc.org/bioc/BioC_2.2_Release_Schedule) 
will result in it being dropped from BioC 2.2. I will provide guidance 
to anybody who needs help upgrading their package.

The changes to Biobase are highlighted in the Biobase/NEWS file. The 
current information in the NEWS file states the changes as:


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




Cheers,
Patrick