[BioC] Agilent's duplicate spots

[Francois Pepin]

Hi Wyatt,

I don't think it is possible to do that. Moreover, only a few probes are
actually replicated on the array. You can look at them as internal
control for consistency.

In our experience, the intensities for all those spots are extremely
close. We actually end up ignoring all but one of them because they are
equivalent. It would also be reasonable for to just average them.

Those are very different from the genes that have several probes
representing them. We tend to see large differences between the
expression of those probes and I would not average them or take an
arbitrary probe to represent the whole gene.

If I didn't understand your question properly, you might want to give us
some more information about the chip and the probes you're talking
about.

Francois

On Thu, 2007-06-07 at 13:16 -0500, 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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