Understanding methyAnalysis Results
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@andrewjskelton73-7074
Last seen 21 months ago
United Kingdom

Hi, 

I'm looking to increase my understanding of the methyAnalysis package results. I've ran through the vignette without much bother, but looking at the DMR table and DM Probes list, I just wondered if there were any detailed explanations of these table headings?

The ones I'm having particular trouble understanding are: difference, tscore, mean_x and mean_y. 

I suspect that the mean_x and mean_y are the mean M values of the given variables specified? The difference is therefore mean_x - mean_y. No idea on tscore.

However, I looked at one probe in the DM Probes table, and looked at the difference (-1.310). Mean_X(-1.011), Mean_Y(-2.3209). Mean_X-Mean_Y= -1.31 == Difference. When I manually extract the means for conditions X and Y, for that particular probe, I actually get mean_X(-2.672) and mean_Y(-2.848) and the difference of those, is not the same as the difference reported. Can anyone shed any light on this?

Also, is there a way to output results using Beta Values? (Providing the current output is M values, correct me if I'm wrong...)

Thanks for any help!

methyAnalysis methyanalysis methylation illuminahumanmethylation450k.db • 807 views
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Pan Du ▴ 80
@pan-du-4535
Last seen 6.5 years ago
United States
Hi Andrew The DMR analysis of detectDMR.slideWin is based on the locally smoothed methylation data. That's why the estimated Difference you get (based on smoothed data) is different from the difference between the original probes (without smoothing). The tscore column basically is the calculated t-score between two comparing groups. Pan On Thu, Mar 5, 2015 at 9:24 AM, andrew.j.skelton73 [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User andrew.j.skelton73 <https: support.bioconductor.org="" u="" 7074=""/> wrote Question: > Understanding methyAnalysis Results > <https: support.bioconductor.org="" p="" 65413=""/>: > > Hi, > > I'm looking to increase my understanding of the methyAnalysis package > results. I've ran through the vignette without much bother, but looking at > the DMR table and DM Probes list, I just wondered if there were any > detailed explanations of these table headings? > > The ones I'm having particular trouble understanding are: difference, > tscore, mean_x and mean_y. > > I suspect that the mean_x and mean_y are the mean M values of the given > variables specified? The difference is therefore mean_x - mean_y. No idea > on tscore. > > However, I looked at one probe in the DM Probes table, and looked at the > difference (-1.310). Mean_X(-1.011), Mean_Y(-2.3209). Mean_X-Mean_Y= -1.31 > == Difference. When I manually extract the means for conditions X and Y, > for that particular probe, I actually get mean_X(-2.672) and mean_Y(-2.848) > and the difference of those, is not the same as the difference reported. > Can anyone shed any light on this? > > Also, is there a way to output results using Beta Values? (Providing the > current output is M values, correct me if I'm wrong...) > > Thanks for any help! > > ------------------------------ > > You may reply via email or visit Understanding methyAnalysis Results >
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Hi Pan, 

Thanks for the reply. Your explanation makes sense, thanks! What's the best way to output Beta values? Would it to be 2^Difference?

Cheers

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Also, is t-score the test statistic from a t-test? 

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Also, is t-score the test statistic from a t-test? 

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Yes. t-score is the test statistic from the t-test. On Fri, Mar 6, 2015 at 2:10 AM, andrew.j.skelton73 [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User andrew.j.skelton73 <https: support.bioconductor.org="" u="" 7074=""/> wrote Comment: > Understanding methyAnalysis Results > <https: support.bioconductor.org="" p="" 65413="" #65456="">: > > Also, is t-score the test statistic from a t-test? > > ------------------------------ > > You may reply via email or visit > C: Understanding methyAnalysis Results >
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