[BioC] CGH analysis without genome positions

[Sean Davis]

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