volcano plot in Limma
Last seen 3.6 years ago
I used the current command in Limma to create volcanoplot, the Y axis is "LogOdds" and X axis is "Log2FoldChange".
I would like to have Y axis as "log10Pvalue". how to do that? please advise
Last seen 3 hours ago
The city by the bay
You can't. If you want to have log-p-values on the y-axis, you'll have to do some ugly hacks, like:
fitmod <- fit # after eBayes()
fitmod$lods <- -log10(fitmod$p.value)
volcanoplot(fitmod, ylab="- log10 Pvalue")
Also see A: Volcano plot labeling troubles for why log-odds are preferred for volcano plots.
Traffic: 488 users visited in the last hour