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!