[BioC] CGH analysis without genome positions

[Daniel Rico Rodriguez]

Hi,

you really need the chromosome and position where the probes map in  
the genome.

You can user readPositionalInfo function in snapCGH package to get  
that information from previously parsed Agilent txt files.

Check the package vignette.

Best,
Daniel

On Apr 6, 2010, at 7:58 PM, Sean Davis wrote:

> On Tue, Apr 6, 2010 at 1:47 PM, adam_pgsql  
> <adam_pgsql at witneyweb.org> wrote:
>>
>> Hi,
>>
>> I am trying to do some CGH analysis with Agilent arrays, but all  
>> the analyses methods seem to require genome position information.  
>> Does anyone know of any packages that will call genes as present/ 
>> absent without the genome position?
>>
>
> I don't think of CGH analysis as "present/absent", but perhaps I am
> not clear on what you mean by CGH analysis.  For Agilent arrays,
> presumably you have two colors, one representing the sample and the
> other the reference.  Simply make a ratio and then rank the probes
> based on that.
>
> Sean
>
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********************************************

Daniel Rico Rodriguez, PhD.
Structural Computational Biology Group
Spanish National Cancer Research Center, CNIO
Melchor Fernandez Almagro, 3.
28029 Madrid, Spain.
Phone: +34 91 224 69 00 #3015
drico at cnio.es
http://www.cnio.es

********************************************






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