I would like to know the exact pvalue Im getting from GSEA. However, GSEA reports a pvalue of 0.0 whenever the value is lower than 1/ # of permutations. The manual recommends upping the number of permutations to get a more specific pvalue, however I would like, if possible, to get the exact pvalue for this number of permutations (1000.) Is there a setting I can change to get the program to output the exact value without rounding it off to 0.0? Thanks!

You will almost never be able to calculate a exact p-value using permutations. To have a chance you would need to be able to calculate through all possible permutations of the data. But even doing so it is possible that you will never have a simulated value as or more extreme than the observed.

If no simulated observations were as or more extreme than observed after 1000 iterations, your real p-value is likely much smaller than your threshold value anyway, so I wouldn't worry about it.

The number of permutation gives you a upper bound on the "real" p-value. If you make 1000 you can say your real p-value < 0.001, if you make 10000 (and the output is 0 again) you can say it is < 0.0001.