Hello, I am confused about how my design matrix should look. I have data from 14 arrays, each with the same common reference in one channel and a sample of interest in the other. There are technical and biological replicates of each sample with wild type and two different mutants as follows: # green red 1 ref wt-A 2 ref wt-A 3 ref wt-B 4 ref wt-B 5 ref wt-C 6 ref wt-C 7 ref mut1-A 8 ref mut1-A 9 ref mut1-B 10 ref mut1-B 11 ref mut2-A 12 ref mut2-A 13 ref mut2-B 14 ref mut2-B I wish to use duplicateCorrelation for the replicate arrays and then ask what genes are differentially expressed in each mutant relative to wild type. Any help is appreciated. Thanks in advance! Matt