[BioC] intended behavior of plotPCA and AffyBatch objects?

[James W. MacDonald]

Hi Jenny,

I never intended plotPCA() to be used with an AffyBatch, so the behavior 
is (now) as intended. Unless your AffyBatch contains normalized PM 
values, I am not sure how useful a PCA plot might be. But maybe I am 
missing something?

Anyway, AffyBatch now extends the eSet class instead of exprSet, which 
as you mentioned is soon to be deprecated. Since an AffyBatch is not 
really an extension of an ExpressionSet (or an exprSet for that matter), 
extending eSet is a more logical choice.

 > extends("AffyBatch")
[1] "AffyBatch"        "exprSet"          "annotatedDataset" 
"VersionedBiobase" "Versioned"
 > R.version.string
[1] "R version 2.4.1 (2006-12-18)"

 > extends("AffyBatch")
[1] "AffyBatch"        "eSet"             "VersionedBiobase" "Versioned" 

 > R.version.string
[1] "R version 2.5.0 (2007-04-23)"

As you mentioned, you can always extract the PM probes and call 
plotPCA() on that. I'm not sure I want to change the behavior of 
plotPCA() to work with AffyBatches (or the eSet class in general), but I 
am always open to reasonable arguments.

Best,

Jim


Jenny Drnevich wrote:
> 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
> 
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
> 
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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