Dear DSS developpers,
First, thank you for your software which is very useful for methylation analysis.
I have a question regarding the application of a delta threshold in callDML or callDMR functions. I have read your explanations in the vignette and help of the functions but I still don't fully understand the concept. I must say that I only have very basic notions in bayesian statistics :p. I don't really understand why the application of a delta threshold give different results than no delta applied but a simple selection of sites with methylation difference above the same threshold. For example, I have generated results for the identification of DMR, first without delta (delta=0), and I obtained 2,184 significative regions. If in these results I apply a filter on Diff.Methy > abs(0.25), I get 1,832 regions. When I apply callDMR specifiying delta=0.25, I only obtain 227 regions. I understand that a posterior probability is computed but I don't really understand why, as a statistical test has already been applied. Could you help me understand please?