how to check significant differential methylation, hypermethylated or hypomethylated betweem case and control groups?

Question

[carlos_marchi]

Hi,

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 absolute 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 hypomethylated? if delta_m < -2

Thanks a lot!

[WouterDeCoster]

have you googled for "differential methylation test" or "differential methylation software"? Please don't do this manually or by writing any test code yourself. This is something for which robust software exists. (e.g. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1664-9)