[BioC] Separate Channel Analysis of Two-Color Data

[Naomi Altman]

You have to be a bit careful here.  Averaging works if all the genes 
have the same number of replicates.  If not, then averaging will 
violate the variance assumptions, although you might be able to 
mitigate this by using spot weights.  On spotted arrays, one usually 
does have the same number of replicates, but on Agilent arrays, it is 
up to the array designer.

--Naomi

At 04:58 PM 12/12/2006, Gordon K Smyth wrote:
>On Wed, December 13, 2006 5:16 am, Weiyin Zhou wrote:
> > Dr. Smyth and limma users,
> >
> > If I want to do separate channel analysis of two-color Agilent data
> > file, how can I deal with replicated spots within array?
> >
> > According to limma User's Guide, Chapter 9, for doing separate channel
> > analysis of two-color data, the correlation to be estimated is that
> > between the two channels for the same spot rather than between
> > replicated spots.   So how can I get one value for the replicated spots
> > within array?  In ratio base, it gets one p value for the replicated
> > spots by use function duplicateCorrelation and ndups=2.
> >
> > I am thinking maybe I should do average of replicated spots within array
> > first, then do intraspotCorrelation to get estimate the correlation.
>
>That's what I would do.
>
> > But I don't know what kind of function available for doing it?
>
>?avedups
>
>Best wishes
>Gordon
>
> >
> >
> >
> > Could you help me?
> > Thanks in advance,
> >
> > Regards,
> >
> > Weiyin Zhou
> > Statistics and Data Analyst
> > ExonHit Therapeutics, Inc.
> > 217 Perry Parkway, Building # 5
> > Gaithersburg, MD 20877
> >
> > email: Weiyin.zhou at exonhit-usa.com <mailto:Weiyin.zhou at exonhit-usa.com>
> > phone: 240.404.0184
> > fax: 240.683.7060
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
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