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Y-axes of Volcano plots

I have a DESeq2 object and generating a volcano plot of up, down and non-sig genes

par(mar=c(5,5,5,5), cex=1.0, cex.main=1.4, cex.axis=1.4, cex.lab=1.4)
topT <- as.data.frame(deseq2object)
with(topT, plot(log2FoldChange, -log10(padj), pch=20, main="Volcano plot", cex=1.0, xlab=bquote(~Log[2]~fold~change),ylab=bquote(~-log[10]~P~value)))
with(subset(topT, padj<0.05 & log2FoldChange>2), points(log2FoldChange, -log10(padj), pch=20, col="red", cex=0.5))
with(subset(topT, padj<0.05 & log2FoldChange<=-2), points(log2FoldChange, -log10(padj), pch=20, col="green",cex=0.5))

The Y-axes looks weird to me, is this normal?Volcano-plot

enhancedvolcano volcanoplots r
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updated by Buffo Buffo • written by Bioinfo_2006 Bioinfo_2006

This plot suggests that some genes have an adjusted p < 10e-300... That is pretty low, you can check in your data if that is true.

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written by Benn Benn

Yes, the data does have pretty low values

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written by Bioinfo_2006 Bioinfo_2006

What do you mean by "weird", from a visual standpoint or rather as Benn says these absurdly small (or here high) p-values?

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written by ATpoint ATpoint

1 answer

It looks like you do not have enough replicates or the dispersion between them is high.

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written by Buffo Buffo

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