I am validating CNV calls using micro arrays. For now I use only CNV probes, but using SNP probes will increase the resolution greatly. Arrays are cytoScan 750k and HD.
How can I utilize snp probes? I have log transformed intensities of snps, usually there are 2 of them per Genomic position. Am I right that I can transform them to overall intensity just using log(exp(x) +exp(y))? X and y here denote intensity of allelic variants. Will the intensity be equal if x and y worked, or 2y, or 2x?
I use non parametric tests, so small differences in intensity will not spoil everything.