[BioC] Multiple class gene finding

[Sean Davis]

I have a dataset with many classes and would like to find the genes
associated (differentially expressed) with each class.  The experimental
design is two-color with a common reference.  I am not interested in
differential expression between the reference and the sample, but only the
differences between samples.  One approach would be to do T-tests between
ratios for each group and all others.  Another would be to use F-statistics
to determine those genes that are differentially expressed in a more general
sense.  What I really want, I think, is a combination of the two so that I
can label each gene with class(es) and know that it is differentially
expressed across samples.  What functions exist for doing something like
this?  I think the limma package provides ClassifyTestsF which looks useful.
Are there others?  Have others used other approaches?

Thanks,
Sean
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Sean Davis, M.D., Ph.D.
National Institutes of Health
  Postdoctoral Research Fellow
    National Human Genome Research Institute
  Clinical Fellow
    National Cancer Institute
Johns Hopkins University
  Clinical Fellow
    Department of Pediatric Oncology
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