I have a normalized data set by Agilent, I want to create a volcano plot for the data.

I am using R to create the plot.

Can someone guide me or send me a link to the code for doing so?

You do need to define a differential expression analysis for the data before it is meaningful to make a volcano plot.

If you have done such an analysis using the limma package, then simply volcanoplot(fit) makes a volcano plot. See ?lmFit for a code example.

Hi,

you can use the 'volcano' function from the EnrichmentBrowser package in case you have your data in an ExpressionSet.

Otherwise you can just use these lines:

I assume <fcs> to be a vector of log2 fold changes and <ps> a vector of e.g. t-test derived p-values:

plot(x=fcs,
        y=-log(ps, base=10), col="red",
            main="Volcano Plot", xlab="log2(foldChange)", ylab="-log10(p)")

Best,

Ludwig