[BioC] intended behavior of plotPCA and AffyBatch objects?

[Jenny Drnevich]

Hi Jim,

I just upgraded to R 2.5 and Bioconductor 2.0, and I noticed a change 
in the behavior of plotPCA. In R 2.4 and affycoretools 1.7.5, plotPCA 
could take an AffyBatch object, even though the help file does say it 
only supports exprSet, ExpressionSet and matrices (I just noticed!). 
I looked through the code, and in Bioconductor 1.9, if 'eset' is an 
AffyBatch object, a call to  ' is(eset, "exprSet")' returned true, 
but in R 2.5 it returns false. The newest documentation for class 
AffyBatch still says it extends the exprSet class, which I know is 
(or will be) deprecated. I guess plotPCA was never intended to be 
called on an AffyBatch object, and I can get around it by using 
pm(eset) in the call, but I did want to point out the change with the 
AffyBatch class. I don't know if this was intended behavior or not, 
or if the AffyBatch class will be updated to extend the ExpressionSet 
class... which makes this more of a general affy question than 
affycoretools, I guess!

Cheers,
Jenny

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

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e-mail: drnevich at uiuc.edu