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 

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,


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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