Hi, On Monday, January 19, 2015 at 3:42:59 PM UTC+2, Sam Padmanabhuni wrote: > > 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. > As far as I know, the out put of CBS is the relative copy number. It does not directly tell you the copy number states.
> > 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? > GLAD can calculate copy number states for affy-array, although I have not used it before. > > 3. Also, do you have a vignette on how to run CRMAv2 and CBS on CytoScan > HD array? This would be really helpful. > It is the same with other chiptype, prepare input as required (there is vignette). BTW, I am also working on CytoScan HD. What kind of analysis are you going to do? Do you have paired samples or non-paired? Maybe we have something common and we can discuss. Br, C.Y > 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.
