How to calculate differential methylation with more than two groups?

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Adeline M

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Sep 28, 2025, 9:27:35 AM (4 days ago) Sep 28

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Hello,

I am new to this field. I tried to find the answer to my question on the group, but I didn't really understand what I read.

I am trying to compare methylation between three groups. I have reached the stage where I need to use the calculateDiffMeth function. It works, but in the end, how can I know how the comparison was made, since there are more than two groups?

more than two groups detected: will calculate methylation difference as the difference of max(x) - min(x), where x is vector of mean methylation per group per region,but the statistical test will remain the same.

Is there a way to specify in the final table what the meth.diff column corresponds to, i.e., group 1 vs. ctl, group 2 vs. ctl, or group 1 vs. group 2?