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  • samseq in samr fdr cutoff

    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:

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

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