Dear Henrik, I have a dataset in which my collaborators took two types of cancer cell lines and made a few single copy clones of them per cell line. The clones were then used for drug resistance study in pairs (i.e. clone treated vs clone untreated). I would like to ask you: 1. whether it is possible to do this kind of analysis (we mostly need copy number changes in the pairs) using aroma.affymetrix and and the cbs model built in your package? 2. which parts of aroma.affymetrix I should use (i.e. how would you do it yourself?) 3. is having the tumor and not the normal reference a big problem in this analysis - would the outcome be reliable? 4. I did the doCRMAv2() on them. Should I treat the two cell lines separately when applying doCRMAv2()?
Kind regards, Marcin -- 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. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
