[Bioc-devel] Farewell to exprSet and phenoData, two deprecated classes

[Seth Falcon]

Hi all,

The exprSet class and the phenoData class are now deprecated in favor
of ExpressionSet and AnnotatedDataFrame, respectively.

It is time to start saying goodbye to these classes and to any methods
that have exprSet or phenoData in their signature.

Package maintainers:

 * If your package defines a method for exprSets or phenoData, please
   add a deprecation warning following the example below.

 * If you see deprecation warnings messages regarding exprSet, please
   start using ExpressionSet instead.



Example (for BioC 2.0, R 2.5.x ONLY):

    OLD CODE
    setMethod("frob", signature(x="exprSet", y="character"),
              function(x, y) {
                   ... # stuff here
              })

    NEW CODE
    setMethod("frob", signature(x="exprSet", y="character"),
              function(x, y) {
                   .Deprecated(msg=Biobase:::EXPRSET_DEPR_MSG)
                   ... # stuff here
              })
      


Best,

+ seth

--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org