[BioC] Single channel CGH analysis [was Re: Bioconductor Digest, Vol 62, Issue 3]
sdavis2 at mail.nih.gov
Fri Apr 4 20:05:24 CEST 2008
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?
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
> 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
> > > 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
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