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 

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.


> 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.

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