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firma
2007 Jul 30
0
problems in limma
...ot;plateau-PLATEAU","PLATEAU-PLAIN")
contrast.matrix
Contrasts
Levels plain-PLAIN plateau-PLATEAU PLATEAU-PLAIN
plain 1 0 0
plateau 0 1 0
PLATEAU 0 -1 1
> fit2MA.pi<-contrasts.fit(fitMA.pi,contrast.matrix)
> fit2MA.pi<-eBayes(fit2MA.pi)
> resultsi.001.fc2=decideTests(fit2MA.pi,method="nestedF",adjust.method="BH",p.value=0.001,lfc=log2(2))
write.fit(fit2MA.pi,
results=decideTests(fit2MA.pi,method="nestedF",adjust.met...