[BioC] LIMMA: Duplicate spots

[Jenny Drnevich]

Hi Cecila,

Yes, this is still true. However, as long as there are the same 
number of replicate spots per gene, you should be able to fake it. 
Once you're done with any location-based normalization, you can 
simply sort your MAlist object so that rows with duplicate spot names 
are right next to each other. You may have to cut out blanks/control 
spots/etc. that have a different number of replicates than all of your genes...

HTH,
Jenny

At 03:04 PM 7/23/2008, Cecilia McGregor wrote:
>Hi All
>
>I haven't used LIMMA for a while, but I remember that when I did
>there was a special way to handle duplicate spots. However the
>layout of the array had to be such that one replicate was printed
>first for all spots and then the other replicate, because somewhere
>you had to say something like there are 5000 spots and the next rep
>starts at spot number 5001. Is this still true? The reason I'm
>asking is because I'm developing Agilent arrays and they randomize 
>everything so it would not be possible to say the duplicate spots 
>start at a specific place.
>
>Thanks
>Cecilia
>
>Cecilia McGregor, Ph.D.
>Department of Entomology
>404 Life Sciences Building
>Louisiana State University
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>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

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