R help - Jan 2005 - limma "ref"

Hi,
I have a question about limma.
I have data from spotted arrays. 
 I have class A and Class B on the same slide. In Limma if I put class 
A as the reference (ref), are the list of genes I get in the output for class A
or
class B?

#design <- modelMatrix(targets, ref="classA")
design


Josephine Brennan

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