I used the R rawcopy package to analyze my affymetrix SNP 6.0 data. This produced the segmentation and the log ratios and allelic imbalance values. Now I'm trying to analyze those, but I can't find a suitable way. I tried the packages that are stated in the rawcopy paper for further analysis and failed to apply any of them. This was mainly because all of them have practical no useful documentation. Or at least I didn't find one. Right now I started trying to calculate the gains and losses with a simple threshold method myself, but even this is tricky because I'm not sure if I use the correct outputs from rawcopy... If anyone has experience with the rawcopy output and its further usage, I would be extremely happy to get some advice.