Hi Sean,

Thanks Sean.
One more question. Do you feel that the experimental design is wrong or it
has some major problems?

Abhilash

On Fri, Apr 4, 2008 at 11:35 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> On Fri, Apr 4, 2008 at 1:56 PM, Abhilash Venu <abhivenu@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@mail.nih.gov> wrote:
> > > On Fri, Apr 4, 2008 at 4:03 AM, Abhilash Venu <abhivenu@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
>



-- 

Regards,
Abhilash

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