[BioC] multiple testing with 54000 genes

[Dipl.-Ing. Johannes Rainer]

hi,

i wanted to ask if someone has experience in multiple testing with a 
large number of genes.

i have in total 24 Affymetrix chips (hgu133plus2), 12 patients, for 
every patient an 0 hours and 6 hours after treatment sample. i 
calculated p values using permutation (mt.maxT function with 
test="pairt") and corrected for multiple testing using the Benjamini 
Hochberg method. the problem is, that with that large number of tests 
(54675 genes and therefore 54675 tests) after adjusting the p values no 
gene shows a "significant" difference.

i will now reduce the number of genes to test to get to some results.
has anyone experienced similar problems?

thanks, jo