[BioC] CGH analysis without genome positions

[Sean Davis]

On Tue, Apr 6, 2010 at 1:58 PM, Sean Davis <seandavi at gmail.com> 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.

I'm making an assumption here that you are using some custom array
based on an organism with no assembled genome.  If there is an
assembled genome, then you should map your probes to the genome using
an alignment tool (blast, blat, etc.) and use those alignments for
more standard CGH analysis.

Sean