Dear All, Dear Dr. Aryee and Dr. Carvalho,

I have a question on interpreting the results of dmrFinder function.

We have performed a CHARM analysis on the data we got from NimbleGen
Promoter Medip Arrays. The data is obtained from each patient before and
after treatment. And after performing CHARM analysis, we got some
differentially methylated regions (DMRs).

As the samples are before and after treatment results of the same patient,
the samples are treated as paired samples.

My question is about interpretation of the results:

After running this:

dmr1_2 <- dmrFinder(rawData, p = p, groups = grp,compare = c("to", "ts"),
cutoff=0.995,paired=TRUE,pairs=pairs)

to: before treatment
ts: after treatment

- For example I have found a DMR like this (I summerized the result for my
question):

chr 8, diff= -0.30427 and maxdiff=0.47935

As the diff value is calculated like this:   average l (logit(percentage)
methylation if l=NULL) difference within the DMR if paired=TRUE

Is it true to say that: "The region has 0.30427 times the risk of being
methylated in samples of after treatment compared to samples of before
treatment."

I know that it does not look meaningful to use the word "risk" when talking
about something like that but I can not find a better way to say it
truely. Is it possible to express it like a "0.30427 fold difference in
methylation"? And also am I interpreting the "-" sign truely?

Thank you for your help in advance,

Best Regards,

Zeynep

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