[BioC] limma

[Josephine]

Hi everyone,
I have a question concerning spotted array analysis and limma.
The analysis is working fine except I'm not sure what the out put means. 
I have sample A and samlpe B on an array (3 replicate slides) and in limma analysis I put sample A as the reference.
 Therefore the results I get, are they the genes up/down regulated due to sample A or sample B?
Josephine Brennan

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