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

[Sean Davis]

On Fri, Apr 4, 2008 at 2:42 PM, Abhilash Venu <abhivenu at gmail.com> wrote:
> Hi Sean,
>
> Thanks Sean.
> One more question. Do you feel that the experimental design is wrong or it
> has some major problems?

Besides losing the advantage of the two-color system, the experimental
costs are approximately double what they could have been if only one
slide and two colors were used.

Sean


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