I am trying to use the dmpFinder() function in minfi. It takes a MethylSet object or matrix. If it's a MethylSet object, it runs getM() on it to generate logit transformed Beta values. That is consistent with the vignette. However, not all preprocess functions yield a MethylSet object. There are also tutorials (such as https://www.bioconductor.org/help/course-materials/2015/BioC2015/methylation450k.html) that use beta values (from getBeta()) as input, which will work regardless of preprocessing. Is one method more correct than the other? Does it depend on the preprocessing?