Differentially methylated site is technically measured by each probe. However, CpG island within gene promoter is comprised of numerous probes. Do we have a consensus of how to determine the methylation level of the entire CpG island (or entire promoter) given the methylation of each probe within the CpG island?
P.S. I ask this because I doubt the biological validity of using Differentially Methylated Region (DMR). DNA methylation impose its impact by suppressing gene expression. When we try to measure the magnitude of DNA methylation, should not we consider more about the detailed correlation between methylation and mRNA expression (things like whether different CpG site have equal contribution on the expression of corresponding gene?) than merely defining statistically methylated region?
Do you mean you wish to summarize multiple values that you may have obtained for a single region into a single, unified metric?
Methylation level is measured as per CpG site (probe). However, we usually want to know the impact of entire promoter on corresponding gene. So we need to somehow summarized the methylation level of each CpG site into the methylation level of corresponding gene. Is there a widely accepted way to do this?