[BioC] Agilent's duplicate spots

[Mcmahon, Wyatt]

Thank you very much, Naomi!  

When you say, "sort by gene so that the duplicates are adjacent in the
data matrix," do you mean by using Excel?

Thanks,

Wyatt

-----Original Message-----
From: Naomi Altman [mailto:naomi at stat.psu.edu] 
Sent: Thursday, June 07, 2007 3:36 PM
To: Mcmahon, Wyatt; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Agilent's duplicate spots

I think most of us have found that the spatial aspect is not that 
important.  Normalize the data and then sort by gene so that the 
duplicates are adjacent in the data matrix.

--Naomi

At 02:16 PM 6/7/2007, Mcmahon, Wyatt wrote:
>Hello everyone,
>
>
>
>I'm new to bioconductor and microarray in general, so please excuse my
>ignorance.
>
>
>
>I am trying to analyze my microarray experiment using limma.  We have
>used Agilent to spot our arrays, and we have duplicate spots.  However,
>these spots are placed randomly over the entire chip.  How do I let
>limma know that there are duplicate spots with a random distribution.
I
>can't seem to find anything that explains this.
>
>
>
>Thanks in advance,
>
>
>
>Wyatt
>
>
>
>K. Wyatt McMahon, Ph.D.
>
>Postdoctoral Research Associate - Functional Genomics Center and
>Services Facility
>
>Texas Tech University
>
>Department of Plant and Soil Sciences
>
>Campus Box 42122
>
>79409
>
>806-742-5073 ext. 263
>
>
>
>
>         [[alternative HTML version deleted]]
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111