Violation of Independence test for differential methylation (DM)
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Hi, it always depend how do you create the contingency table, but I think the idea is that neighbooring CpG positions have correlated methylation levels and simply summing them up (or testing them one by one and then applying a simple FDR correction) is not taking this dependency into account.
Thanks for explaining. But when a single CpG site was tested, the contingency table sums up the (normalized) methylation counts of this CpG site from each sample (patient). I thought the independence we are looking for is the methylation level of this site between different samples, right?