Calculating a p value by permutation analysis
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chris86 ▴ 420
@chris86-8408
Last seen 4.3 years ago
UCL, United Kingdom

Hi

I am calculating gene correlations for all patients gene expression data against clinical parameters. Then I want to derive p values by permutation. Is it OK to randomly permute the sample columns and then re calculate the correlation for every gene N times. Then ask how many times are correlations observed equal to or greater than a genes correlation by chance?

E.g. If my correlation is 0.3

Then the p value would be, n obs > 0.3/ total obs

So I have one distribution per gene?

Thanks,

Chris

microarray • 3.2k views
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@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

You p-value computation isn't quite correct, see:

"Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn" at http://www.statsci.org/smyth/pubs/permp.pdf

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