I am using limma for the first time (and by the way, I think it is a really cool tool for Diff. Expr. gene detection :) ).
I have 12 samples: 4 biological replicates x 3 technical replicates for each of them. So, my setting is something like:
A A A B B B C C C D D D
I want to find the genes that are differentially expressed between condition A and all the rest conditions. I am using the contrast A-(B+C+D)/3 in my contrast matrix. I would like to ask if this is correct...I am not sure about it.
Thank you very much in advance!