[BioC] Agilent's duplicate spots

[James W. MacDonald]

Hi Wyatt,

Mcmahon, Wyatt wrote:
> 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?

That's a joke, right? If not, you need to sit down and read 'An 
Introduction to R'. Right now. Really.

You could sort using Excel, but that would be like using the butt-end of 
a screwdriver to pound a nail when you have a hammer hanging on your 
belt. You could do it, and eventually you would get the job done, but 
you are really using the wrong tool for the job.

Best,

Jim


> 
> 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
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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