Hi - I am looking for help with how to account for duplication at 2
levels in analysis using lmFit in limma of data from a 2-channel cDNA
microarray (for which ImaGene software was used for analysis).  The
array is a 4 x 4 block of 24 rows x 24 columns of spots.  The array> has
been duplicated on the top half and the bottom half of the slide. 
Furthermore, the spots themselves have been duplicated side-by-side. 
Thus, each slide has 4 replications of the same EST, occuring in 2
adjacent pairs that are equally separated.  My reading of the limma
vignette and elsewhere on within-array duplicate spots hasn't yielded a
solution.  I've tried using the ndups options in lmFit and
duplicateCorrelation.  While I have been successful with accounting for
duplicate spots, I haven't been able to find a solution for the
replication of the arrays on the same slide, where each array has
within-array replication.  
 
Does anyone have any experience or advice?  Thanks - Noah Cohen

 
Noah D. Cohen, VMD, MPH, PhD, DACVIM
Professor
Department of Large Animal Clinical Sciences
College of Veterinary Medicine and Biomedical Sciences
Texas A&M University
College Station, Texas 77843-4475
Telephone: 979-845-3541
Fax: 979-847-8863
e-mail: ncohen@cvm.tamu.edu

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