Question: Y-axes of Volcano plots
0
gravatar for Bioinfo_2006
17 months ago by
Bioinfo_2006140
Bioinfo_2006140 wrote:

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

ADD COMMENTlink modified 17 months ago by Buffo1.8k • written 17 months ago by Bioinfo_2006140
1

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.

ADD REPLYlink written 17 months ago by Benn8.0k

Yes, the data does have pretty low values

ADD REPLYlink written 17 months ago by Bioinfo_2006140

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

ADD REPLYlink written 17 months ago by ATpoint44k
0
gravatar for Buffo
17 months ago by
Buffo1.8k
Buffo1.8k wrote:

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

ADD COMMENTlink written 17 months ago by Buffo1.8k
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