[BioC] Factorial design with two-channel microarray data with Limma
Eran Tauber
etauber at eudoramail.com
Wed Oct 7 09:48:26 CEST 2009
Dear Gordon,
Many thanks for your prompt reply. The User Guide and section 8.1.1 describes
a simple comparison between two strains hibridized to the same array. In my
experiment there are two factors, strain and treatment where for each strain,
the two treatment were hybridized to the same array (see original post). My
understanding was that my case resembles more example 8.7 in the manual, and
my goal is to identify the genes that respond differently in one strain
compared to the other (the interaction term, following the manual, question 3,
p.44). The problem is that section 8.7 demonstrates it with Affymetrix data
and I'm not sure how to apply it to a 2-channel experiment. Please advise, Eran
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