Dear AromaAffymetrix Team, First of all, thank you very much for such a detailed vignette on how to perform the CNV analysis.
I am Sam, a PhD student in genetics, working on CNV analysis on data from CytoScan HD Array. I have read the vignette to do CRMAv2 and non-paired CBS. I have copied the commands and ran in R. But, I have few questions regarding CbsModel and GladModel in segmentation algorithm: 1. It is mentioned that, copy number states is not calculated in CbsModel segmentation. How do I get information of whether the segment is a loss or gain from output of CbsModel? I mean can this information be passed to other algorithms to estimate copy number state. 2. I have looked in to GLAD model and it is mentioned that it is developed for aCGH but my data is not from aCGH. Can it be still used to calculate copy number states for the data I am working on? 3. Also, do you have a vignette on how to run CRMAv2 and CBS on CytoScan HD array? This would be really helpful. Thank you, Best, Sam. -- -- 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/ --- 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 aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
