I'm working with a non-model species so having genes' name is luxury I can't afford. I have my design matrix and choose one combination I'm interested:
cont.matrix1 <- makeContrasts(GlandvsRoot=Leaf - Gland,levels=design)
fit.cont <- contrasts.fit(fit, cont.matrix1)
fit.cont <- eBayes(fit.cont)
fit.cont <- eBayes(fit.cont)
summa.fit <- decideTests(fit.cont)
summary(summa.fit)
and when I wanna see the volcano plot:
volcanoplot(fit.cont,coef=1,highlight=100,names=fit.cont$ !!!!!! , main="B.PregVsLac")
in fit.cont$, there is no list of the transcript IDs there so I can use as names for the top 100 hits.
Your comments and opinions are appreciated and valued highly.