[BioC] Limma: technical replicates in multi-group design

Adam Kiezun akiezun at gmail.com
Thu Mar 25 17:51:37 CET 2010

How do I write the design matrix to specify technical replicates in
multi-group experiment on a single-channel array (data coming from

I have 3 groups of samples (A, B, C), each group has 2 technical
replicates (so I have 6 expression vectors: A1, A2, B1, B2, B3). How
do I write the design matrix to tell limma that A1 and A2 etc are
technical replicates and that I want to do all pairwise comparisons
between groups (ie. AvsB, AvsC, BvsC)?

The limma manual covers technical replicates for two-channel arrays,
and the multi-group experiments with biological replicates. I'd like
to know how to deal with a one-channel arrays, multi-group experiment
with technical replicates.


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