**20**wrote:

Hi all, I am a little confused about how to calculate FDR after permutation F test.

Assume there is 6000 genes in my data. And for each gene, I perform 1000 permutation F test and got 1000 F value, which includes 1 original F value and 999 permutating F value. And p-value = sum(F > F-original)/1000.

But I am confused how to calculate FDR? I think it should be FDR = False positive gene number/ gene with Permutation p < 0.05 number.

Thank you in advance:)

**22k**• written 3.0 years ago by hellocita •

**20**

Hi! Did you find answers for the questions you asked? To my understanding for each gene you have to calculate: perm_p-value= number of p-values<=p-value experimental +1/total number of permiutations+1. So your formula is not correct in this way. To perform

`FDR`

correction you should take your raw`p-values`

and adjust them e.g. by means of`p.adjust(method='fdr')`

`R`

base function.170