Deriving p values for gene correlations by permutation analysis
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6.0 years ago
chris86 ▴ 370

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,

Robert

RNA-Seq next-gen • 2.1k views
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It sounds about right to me. Have a look also at the boot package in R (and this FAQ  http://www.ats.ucla.edu/stat/r/faq/boot.htm). Once you have the pvalues, I guess you should correct them for the multiple tests you performed (i.e. one test per gene).

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Yeah I hadn't done multiple testing correction, that is a good point

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