0
$\begingroup$

I am reading from this where they mention running 500K fisher exact test to find significant associations between different DNA changes and a phenotype.

They also mention that Bonferroni, Benjamini, and FDR can be used to set a significance threshold, which I think I understand.

What I don't get is that they say permutation can also be used to set a significance threshold. How can you use permutation on fisher exact test output to set a significance threshold?

$\endgroup$
0
$\begingroup$

It's difficult to speculate they mean without giving a citation or reference, but they may be referring to the Westfall-Young method which is a permutation based method. I did just answer a question at CV where I suggested using permutation testing (empirical p-value testing), which is here.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.