Hi Michael,

I think the issue here is based on what we wish to make inference about.  The
multiplicity here is the number of pathways, NOT the number of individual
genes. SAM accounts for multiplicity of the latter, not the former.

Debashis


On Sat, Oct 18, 2008 03:34 PM, "Michael Gormley" <michael.gormley@gmail.com>
wrote:
>
In the paper and vignette describing the globaltest package, the
>authors mention the need for multiple testing when testing large
>numbers of pathways or functional gene groups.  While I agree the
>number of statistical tests does need to be accounted for, I do not
>understand the need for additional multiple testing correction if the
>permutation method of calculating p-values is used.  This method is
>used often to approximate the false discovery rate, most notably in
>the original implementation of Significance Analysis of Microarrays
>(SAM).  Am I on track with my assessment here or is the additional
>multiple testing correction used as a more accurate way of obtaining
>the true FDR?
>
>Thanks,
>Michael Gormley
>
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>

Debashis Ghosh
Department of Statistics and Huck Institute of Life Sciences
514A Wartik Building
Penn State University
University Park, PA 16802
Email: ghoshd@psu.edu
Phone: (814) 863-9886
Fax: (814) 863-6699






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