volcano plot in Limma
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mheydarpour ▴ 10
@mheydarpour-9430
Last seen 2.8 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

 

Thanks, Mahyar 

limma volcanoplot • 686 views
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Aaron Lun ★ 27k
@alun
Last seen 4 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.

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Thanks Aaron, It works very well.

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