[BioC] adjustment for dependent hypotheses when pairwise testing

Naomi Altman naomi at stat.psu.edu
Fri Jan 13 22:57:28 CET 2006

I do not think you will be able to use these methods with such a 
small number of genes.  A large number of genes are required to estimate pi0.


At 07:52 AM 1/13/2006, pmt1rew at leeds.ac.uk wrote:
>Dear all,
>I data for 13 genes with the samples from 4 different tissue 
>types.  Would like
>to compare the normal means of the different tissue types using pairwise
>testing with an adjustment for fdr.
>Having considered the Benjamini and Yekutieli reference on the p.adjust help
>page I am unsure as to whether my dependency structure satisfies the criteria
>to just use the regular "BH" adjustment or if  the "BY" adjustment would be
>more appropriate?
>Any suggestions for me please?
>Many thanks
>Rebecca Walls
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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