Hello listmemebers, I have data from two-color microarray expression profiling experiments where 3 whole brain (WB) samples were compared to 3 Mauthner Cells (MC) in a loop design (-> MC #1 -> WB #1 -> MC #2 -> WB #2 -> MC #3 -> WB #3 -> MC #1 ->). In addition to phenotype analysis I would also like to run an individual analysis making all pair-wise comparisons. I'm using the LIMMA package in R to do this. The problem is that the contrast matrix that you have to set up requires that one of the samples be designated as a reference, but in doing so you lose the sample. My question is this, is it possible to run individual analysis with this data set without losing one as a reference point? Many thanks in advance, Dmitriy [[alternative HTML version deleted]]