Dear all, I am quite new to microarray analysis and R in general and to aroma.affymetrix in particular. I am trying to use aroma.affymetrix for paired (tumor vs. peripheral blood) analysis of total copy number with SNP6.0 arrays. The Instructions I find here are for unpaired analysis (SNP6.0). For paired analysis I only find an example for 250K array sets. So far my strategy was to follow the SNP6.0 example until (including) PCR fragment length normalization. After that I thought to continue with "Identificaiton of copy-number regions in tumor-normal pairs" from the 250K example page. My problem now: I have not quite understood yet how to adapt the commands for use with SNP6.0 arrays. How do I specify which samples belong together? Any help would be greatly appreciated! Peter. --~--~---------~--~----~------------~-------~--~----~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
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