Hi Mira, If the map you provided is of uncorrected p-values at say p=0.05, then you appear to have just a couple small regions of group differences, so it isn't surprising that after FDR nothing would survive.

The result is what it is, and unless you had specific a priori hypotheses regarding regions that would be involved (i.e., to which you could restrict your testing), then there isn't much you can do.

cheers, -MH

On Fri, 2010-10-22 at 14:53 -0700, Mira Michelle Raman wrote:

Hi, I have a dataset that seems to have some very nice group differences (please see the graph and qdec image), but they never seem to survive FDR. I noticed when I run the "Set Using FDR", it generates a very high threshold above 5; where as, with some of my other datasets FDR is set much lower (often in the 2's and 3's). Can you please give me some insight into why the threshold is being set so high? Is it solely linked to the small sample size, or is there something additional we can do in the processing, so that regions with such large group differences will survive correction?

Thank you, Mira

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