Hi,

I'm trying to analyse data from a microarray experiment which consist in
three mutants compared to wild type in a connected design (the experimental
design is like in a 2x2 factorial design) with limma.
When I do the analysis like in a factorial design (page 45 of the manual) I
get a number of differentially expressed genes considerably lower than when
I do separate channel analysis (page 50). From a biological point of view,
for me it makes sense the new genes that I found with separate channel
analysis, but I don't know if this kind of analysis (separate channel
analysis with connected design) is right from a statistical point of
view. What do you think?
Thanks!

Luis.

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