q_value in cuffdiff results

Question

[wangdp123]

Hello,

Does anyone notice that when running twice cuffdiff software for the same dataset, the resultant q_value could be slightly different (not exactly the same)?

Is this normal? Why could this happen?

Many thanks,

Tom

[h.mon]

I don't know the internals of cuffdiff, but the fact it has a --seed parameter strongly suggests it is non-deterministic. Set the seed and then check if results are identical.

--seed value of random number generator seed [ default: 0 ]