How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)

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



      
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