[BioC] Separate Channel Analysis of Two-Color Data

[Gordon K Smyth]

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