Hi,

Is it possible to correct for batch effects in limma when doing a paired analysis? I have pairs from two 
runs Batch 1 and Batch 2. There  are no pairs where one is in Batch1 and the 
other in Batch 2. If I enter the Batch no. into the design matrix, 
no coefficients are generated as there is no difference between run no. 
for any pair.

Any advice on this would be most appreciated.

Thanks,
Khadeeja

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