[BioC] limma model to treat replicate spots

[Joyce Gu]

Hello,
I have cDNA, I tried limma to do normalizeWithinArrays, but the results looks 
like they did not aveage spots. Each spot was printed twice in my cDNA array, 
how limma average them? I have all the log ratio from every printed spot(twice 
printed). When I did correlation between replicated, their coef is very low, 
which compared to arrayTool analysis, is significant different. When I looked 
at the log ratio, limma has twice as many as arrayTool log ratio, so I think 
limma did not average my spots.

Any idea and suggestion is greatly appreciated!

Thanks

********************************
Joyce Gu   M.S.
Scientific Programmer

Cancer Genomics Group
Baylor College of Medicine 
Phone: 832-824-4680
Fax: 832-825-4038