Assigning the name of top 100 DE transcripts/genes to Volcano plot
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Mohammad • 0
@faf1c3a8
Last seen 14 months ago
United States

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.

limma DEGreport Volcanoplot • 552 views
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Entering edit mode
@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

Duplicate question has been answered here: Extracting the tophits from limma Volcanoplot and issue with geneIDs

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