
Hi all,

I have an unusual microarray design. The experiment is meant to compare two conditions. We have 4 slides of microarrays: all four considered as biological replicates. However, one slide contains 2 replicate arrays (we named top and bottom). These two come from the same culture. The design was made this way for frugality. So in total we have 8 samples. I read the limma user guide and there was no example of such design. There are duplicate spots in each array but in random fashion so there is no way to compute the duplicateCorrelation command. I wonder how would I build the design. Any help is appreciated.

Yolande

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