I have DNA methylation samples from two groups of patients (case, control) where I would like to know if the differential methylation is significant and it is hypermethylated or hypomethylated.
Check differential methylation is significant:
pvalue < 0.05 and Delta M?
Is it correct to calculate delta M like this:
Delta M = mean(case_levels) - mean(normal_levels)
What it Delta M threshold? Is |delta_m| >= 2?
How to know the region is hypermethylated or hypomethylated?
hypermethylated if |delta_m| >= 2 otherwise hypomethylated?
Thanks a lot!