Good morning!

Thanks a lot for your answer. 

I am running the FDR with 500 000 permutations, but you are right to be in the safe side I will increase to 1000 000.

My question about the thresholding is about the matrix NBS.test_stat. If I understood well this matrix represent the t (or f) values before the permutations. However, some of my FDR significant edges have very small value (<1) in the NBS.test_stat. So I was wondering if I should discard them afterwards when the t- or f-values are too "weak".

Thanks a lot for your help

Cecile