[BioC] Single channel CGH analysis [was Re: Bioconductor Digest, Vol 62, Issue 3]

[Sean Davis]

On Fri, Apr 4, 2008 at 1:56 PM, Abhilash Venu <abhivenu at gmail.com> wrote:
> Hi Sean
>
> Thanks, I am using arrary CGH from Agilent (244K), which is custom designed
> using their earray software. In one array slide I have hybridized my test
> sample and I would like to compare the same with a reference which i have
> hybridized in another slide.
>  Can you advise on this scenario?
>
> Abhilash

Hi, Abhilash.  It is unfortunate that the experiment was performed
this way.  That said, you can certainly make a ratio of the signal
from each of the two arrays and treat it as 2-color CGH.  Once you
have log ratios, any of the typical CGH analysis packages could be
applied.

Sean


>
> On Fri, Apr 4, 2008 at 5:21 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> > On Fri, Apr 4, 2008 at 4:03 AM, Abhilash Venu <abhivenu at gmail.com> wrote:
> > > Hi all,
> > >
> > >  I would like to find out the methods for analysis of single channel
> array
> > >  CGH. Can I perform the same with CGH package? Or is there any better
> way to
> > >  explore the possibility?
> >
> > Hi, Abhilash.  Generally, you will want to start a new message and not
> > reply to another message when writing to the list.
> >
> > As to your question, you will need to be specific about what array
> > platform you are using.
> >
> > Sean
> >
>
>
>
> --
>
> Regards,
> Abhilash