Hi, I am new to the copy number analysis and i am trying to do the estimation through affymetrix's 6.0 snp array through oligo package. The problem is I couldn't find the method that actually does the analysis, even though there is a data object that hold the results: -------------- next part -------------- A non-text attachment was scrubbed... Name: pastedGraphic.pdf Type: application/pdf Size: 64943 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20080718/5aa469ca/attachment.pdf> -------------- next part -------------- Am I missing something? Or the crlmm does the copy number too(as my understanding it just makes genotype calls). Or should I use other package(?) to do the analysis? Thanks, yupu