I am using dmpFinder to find dmp on a methylation experiment.
As the authors said, dmpFinder is a wrapper around limma, so I tried to emmulate the steps (that I thought) were followed by the dmpFinder function... After examining the function @HansenLab's Github I found a series of steps that I don't fully understand...
Is anyone able to explain the statistics behind the dmpFinder function in minfi package? Why does dmpFinder applies bayes in some cases, or else, uses Sigma?? (Please, follow the link to Hansen's Lab to see the code I am talking about...) Could someone, please, guide me on why these steps are followed? or what do they mean?
I am sorry if the question is too basic, maybe it is a matter of the limma package, but I can't seem to find the answer.
Many thanks in advance.