I'm using the aroma.affymetix R package to do the segmentation of several normal genome Affymetrix 6.0 chip CEL files (arrays of log2 ratios and B allele frequencies). My goal is to generate absolute CNV (+/-) calls to do Fst calculations between populations. The problem is that the output I have from aroma gives me the segment data (start site, stop site, mean log 2 ratio, ect.), but not an absolute CNV state call. Does anyone know of an aroma command/tool that uses a statistical or algorithmic approach to generate the CNV calls? Or is there another package out there that could take the output from aroma.affymetrix and generate the calls from there?
thank you, -Michael