samseq in samr fdr cutoff

[narges]

Hi,

I wanted to ask about the parameter: fdr.output. I was supposed that it is a cut off for the FDR but te problem is that I have run this method twice with different fdr.output but there are some genes which has different FDR in different run. So first I run this:

samfit <- SAMseq(counts, group , resp.type= "Two class unpaired", nperms= 1000, random.seed=1234567, fdr.output=0.05)

And then run :

samfit <- SAMseq(counts, group , resp.type= "Two class unpaired", nperms= 1000, random.seed=1234567, fdr.output=0.1)

I was suppose to get more genes with a larger FDR but I expected that common genes have the same FDR in different runs but it is not like this. So I have some genes which have totally different FDR in different runs.
Why is that so?
Thank you in advance