Results changing a bit every time I run ChAMP

[MRM]

Dear Tian:

I have tried to

set.seed(somenumber) at the very beginning of my program, but still I get slightly different set of DMPs every time I repeat the run. Is there a place in ChAMP program to set the seed so that I get the same result every time on a data set. I use parallel processing using:

library("doParallel")
parcl <- makeCluster(2); registerDoParallel(parcl)

Could that be affecting the results. Thank you very much.

Mano