Entering edit mode

mpg33@drexel.edu
▴
90

@mpg33drexeledu-1897
Last seen 8.1 years ago

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