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Re: st: permutations
Am 17.03.2008 um 17:49 schrieb David Airey:
The p value is simply p=c/n in the tabled results. It is 0.002, and
0.000. Increase your number of permutations if you want something
more exact than 2/1000, or 0/1000. Try 10,000 permutations, instead
of 1000. You should try to report an exact probability. This is
especially important if you are running many SNPs and later want to
apply a multiple test correction procedure. There, 1x10-6 or 1x10-7
matters a lot.
The seed is necessary for replication. If you don't set the seed you
will get chance variation in your results, because permute will be
using different random numbers; setting the seed makes permute use
the same random numbers. It will not affect your statistical
conclusions. Most people will seed the random number generator.
Dave,
thank you very, very much.
Your comments where really helpful!
Regards,
Chris
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