Hello, I have two questions regarding cnv analysis using CytoscanHD data.
1) I am currently implementing PSCBS on my Cancer datasets. This tool looks quite interesting to me. However, what to do you say about giving exact values for calling copy number gains and losses? Can you suggest any thresholds? Any values above 4 would be high copy gains and near zero would be deletions? I have a dataset of more than 200 hundred lung cancer samples so I want to apply significant testing on cnvs. Does GISTIC type algorithms will work on the attached example file? Or any other method you suggest 2) Is tumorboost works with cytoscanHD data? Thanks -- -- 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 [email protected] To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. For more options, visit https://groups.google.com/d/optout.
