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!

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

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

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