[BioC] limma

[A.E.Schiel at lumc.nl]

Hi Josephine,
 Since you already have an answer I was wondering if you could tell me what you mean with having sample A as a reference? Did you define it as the Cy3 labelled sample in the targets file (and if you had a dye-swap what would that mean then?)? Since I was wondering about the meaning of the M-values just like you I am now somewhat confused not knowing exactly what my reference is if I have a dye-swap experiment (pretty much the same as the Bob-example!)

Anja


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