If the spots are plotted adjacent to each other within the blocks you can use a spacing of 1 in your layout and ndups of 3.

Otherwise you can order the MAlist object on the feature ID after you've performed the normalization steps, and then use a spacing of 1.
You probably will have to do this too if your array contains control spots that are not plotted in triplicate. In that case you will have to remove these spots from the object before you do the analysis.

Only the normalization functions in limma use spatial information, so you don't have to be afraid to lose information by doing the ordering.

Regards,

Jan Oosting


-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch on behalf of Brooke-Powell, Elizabeth
Sent: Fri 09-Sep-05 5:27 PM
To: BlueFutures@yahoogroups.com; bioconductor@stat.math.ethz.ch
Subject: [BioC] Triplicate printing and limma
 
Good Morning,

 

I am writing to ask some advice. We are presently printing a 39,000 feature
array and I need some help. We are printing with the triplicates in the same
block and I cannot figure out how to get them out of the same block. It is
making limma analysis very difficult as the program seems to be designed to
analyze printed replicates in different blocks. Can anyone help me in
figuring out how to arrange my 96-well plates of oligos and or a get around
for limma?

 

Thank you for your help,

 

Liz Brooke-Powell 

 

Washington University Medical School, 

Department of Molecular Microbiology,

CB#8230, 660 S. Euclid Ave

St. Louis, MO, 63110 


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