Question: Understanding methyAnalysis Results
0
gravatar for andrew.j.skelton73
4.5 years ago by
United Kingdom
andrew.j.skelton73320 wrote:

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!

ADD COMMENTlink modified 4.5 years ago by Pan Du80 • written 4.5 years ago by andrew.j.skelton73320
Answer: Understanding methyAnalysis Results
1
gravatar for Pan Du
4.5 years ago by
Pan Du80
United States
Pan Du80 wrote:
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 >
ADD COMMENTlink written 4.5 years ago by Pan Du80

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

ADD REPLYlink written 4.5 years ago by andrew.j.skelton73320

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

ADD REPLYlink written 4.5 years ago by andrew.j.skelton73320

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

ADD REPLYlink written 4.5 years ago by andrew.j.skelton73320
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 >
ADD REPLYlink written 4.5 years ago by Pan Du80
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