Re: permutation p value vs. normal p values

We have follow-up information (survival time and censoring) for each
patient, so we can use Cox regression to evaluate the correlation of
each gene's expression levels with patient's survival. The sample size
is indeed small, but that's what we have right now. The actual number
of genes is 15338, so by chance alone, I would expect 15338*0.05=767
genes with a p value less than 0.05. With permutated p values, I had
763 genes with a p value less than 0.05, so they are very very close.
Does this mean the permutations I did really generated a good
distribution under the null hypothesis? What puzzles me is that the p
values from Cox using normal distribution only produced 2 genes with a
p value less than 0.05. What would be the reason for this difference?

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