Dear Tim,

Thank you for your answer. But to my understanding, if I could get this
answer by undoing the logit function (I tought you were doing this), we
should use inverse logit function. Which is exp(x)/(1+exp(x))

And in my case it gives:

> exp(-0.30427)/(1+exp(-0.30427))
[1] 0.424514

Ok, this seems reasonable. And it makes sense how you put this into words.
But if we could use this one as a methylation measure, why would the
creators make things more complicated and convert the value to a logit
value? So, again, to my understanding, I shall learn how to interpret the
diff thing.

Thank you again,

Best :)

Zeynep

On Fri, Aug 17, 2012 at 6:29 PM, Tim Triche, Jr. <tim.triche@gmail.com>wrote:

> Perhaps "on average this region has an
>
> R> 1 - exp(-0.347)
> [1] 0.2931947
>
> approximately 29.3% relative decrease in cytosine methylation after
> treatment?"
>
>
>
> On Fri, Aug 17, 2012 at 1:56 AM, zeynep özkeserli <
> zeynep.ozkeserli@gmail.com> wrote:
>
>> 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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>>
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>>
>
>
>
> --
> *A model is a lie that helps you see the truth.*
> *
> *
> Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>
>

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