**10**wrote:

Hello friends,

I see that it was discussed here: A: Dmr (Differentially Methylated Regions) Identification Software but I would like to dig a little deeper into that, because I couldn't find a satisfying answer yet.

So - what statistical test would you choose for DMR (differentially methylated regions) annotation? Meaning you have a 2X2 table with column labels `WT` and `mutant`, and row labels `methylated` and `not methylated`, each cell has a count for a single region. You need to test whether methylation is dependent on the mutation.

I see that `methylkit` uses Fisher's Exact Test, but that test doesn't make sense to me. Why would DMR's behave hyper-geometrically? This assumes that the background set from which you sample is finite, right? And that's not the case with methylation - you can (theoretically) sample as much as you want, like coin flipping.

Am I right? What test would you use?

Thanks a lot, Amit

If the no-replacement aspect of Fisher's test is what you don't like then just do a binomial test instead. Having said that, the two approach each other with increasing N. Having said that, Charles' answer makes much more sense than a Fisher's or binomial test.

96kThank you Devon.

What do you think is the appropriate test for DMRs with a fixed-size window?

Amit

10