[BioC] globaltest mulitple testing correction

Michael Gormley mpg33 at drexel.edu
Sat Oct 18 21:35:58 CEST 2008

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?

Michael Gormley

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