%meth difference for defining DML with methylKit

[yaaminiv]

In my Cv paper, I defined DML as CpGs that are 50% different between treatments and q-value < 0.01 identified by methylKit. I've seen some vertebrate papers that use a 10% or 25% difference between treatments to define DML (ex. Mac's salmon paper). I believe Claire also used a 25% difference in methylKit (doi.org/10.1101/012831).

Should I use a 25% difference instead of 50%? I could easily try both and see what happens, but I want to know if there's a clearer rationale for picking 25% vs. 50%.

[sr320]

I would try both, no clear rationale as we know the biological signficance of neither.

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