I am analyzing methylation data, I have two files with beta values one for disease samples and another for control samples.
I would like to convert both disease and control beta values in to M values and calculate Fold change of disease/control using M values
I checked many articles and found that in some studies only beta values were used and delta B was calculated to assess DMR.
I tried both ways in the following example and found that different ways could give different assessemnt for a probe or position but i got different results
FC=M_disease/M_control=3.528893 which is differentially methylated in case threshold is 2 fold
delta B=.73-.57=.0.16 #NOT differentially methylated in case threshold=.2
Any one has an experience which has more robust output, using either delta B or FC for instance or using p-value of statistical tests as implemented in many R packages.
Any help is appreciated