I am looking for DNA methylation differences in a case/control experiment; all samples were run on 450k arrays. I am using the minfi package to analyze the data, and normalizing it with the preprocessFunnorm function. All the cases have a copy number variation (CNV) encompassing multiple genes.
1) Should I expect to see difference in methylation for the probes contained within the CNV (due to the different copy number) or would the difference in probe intensity between cases and controls be normalised?
2) If I the observed difference in methylation observed is due to the copy number difference, is there an approach to look at the methylation of these CNV probes per chromosomal copy (apart from dividing beta values by the number of copies)?
Thanks in advance,