Question: Deriving p values for gene correlations by permutation analysis
gravatar for chris86
5.1 years ago by
United Kingdom, London
chris86350 wrote:


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?



rna-seq next-gen • 1.8k views
ADD COMMENTlink written 5.1 years ago by chris86350

It sounds about right to me. Have a look also at the boot package in R (and this FAQ Once you have the pvalues, I guess you should correct them for the multiple tests you performed (i.e. one test per gene).

ADD REPLYlink written 5.1 years ago by dariober11k

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

ADD REPLYlink written 5.1 years ago by chris86350
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