I am using the qvalue R package to calculate qvalues of out of this pvalues distribution:
The lowest qs are around 0.22.
If we have a look at the p-values histogram, we see that there are actually more low ps than expected by chance. But with a q cut-off at 0.15 there is only one marker resulting as significant. When raising the threshold to 0.25 instead, the number of significant tests raise to 10'000.
I think this is due to the fact that low ps frequency decreases toward 0, therefore making it not possible to calculate respective qvalues.
How do you interpret this? Is there a way to obtain a qvalue in this situation?