Logistic regression in methylKit

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Moshe Olshansky

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Mar 25, 2026, 8:44:59 PM (8 days ago) Mar 25

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Hello,

I have two questions regarding logistic regression:

1. If I am only looking for individual CpGs and no overdispersion correction is applied, why a ChiSq or F test is needed? Don't we get the p-values from logistic regression itself?

2. What is meth.diff? Is it the difference between the estimated logIt? If so, how would you estimate the difference between the methylation proportions?