[BioC] array CGH

[Mark Dunning]

Hi Lisa,

The snapCGH package might be a good place to start because it allows you to 
try out methods from the most common CGH packages (GLAD, aCGH, DNAcopy 
etc..) and displays the results in a common format, allowing for easy 
comparison.

Regards,

Mark

On Oct 13 2006, Lisa Luo wrote:

>Dear List,
>
> I have a set of BAC array CGH data to analysis. I am new to this kind of 
> analysis. Could anyone please recommend me a good package?
>
> I read some papers on aCGH. For the size of BAC clones, is averaging a 
> few probes a good idea? I tried DNAcopy and I am not happy with the 
> results either. Another question: Can we use the ratio to call it 
> amplification or deletion? In my normal samples, I should expect ratio to 
> be about 1. But ratios in some probes/chromosomes tend to be high and 
> ratios in another probes/regions tend to be lower. So how to use the 
> ratio?
>
>Thank you so much for your help!
>
>Lisa
>
> 		
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-- 
Mark Dunning
PhD Student
Computational Biology Group
Hutchison / MRC Research Centre
Department of Oncology
University of Cambridge
Hills Rd, Cambridge CB2 2XZ

Email  : md392 at cam.ac.uk
Phone : +44 (0) 1223 763380