I have samples that are processed in three ways: whole genome seqeuncing, whole exome sequencing, and infinium SNP array. I'm looking for suggestions on how I could compare these data to see how much variance there exists simply due to using different technologies. Specifically, I'm interested in copy number analysis. My initial thought is to obtain the log ratios for each and then see the correlation in log ratio between different methods. I can get the log ratio for SNP array data, but I don't know how to do it for WGS or WES. Has anyone done something similar in the past? I also can't seem to find any recent work that has done this kind of work before, so I would appreciate any pointers.