Question: Deriving p values for gene correlations by permutation analysis
0
gravatar for chris86
4.4 years ago by
chris86340
United Kingdom, London
chris86340 wrote:

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 • 1.6k views
ADD COMMENTlink written 4.4 years ago by chris86340
1

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).

ADD REPLYlink written 4.4 years ago by dariober11k

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

ADD REPLYlink written 4.4 years ago by chris86340
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 657 users visited in the last hour