I have highlighted the different points in my volcano plot according to their probe type i.e. miRNA, snoRNA etc. with the row names of the microarray data as follows:

renderPlot({volcanoplot(fit, col=as.factor(getType(rownames(MA))), names=rownames(MA), legend=as.factor(rownames(MA)), main="Volcano")})

The part highlighted in yellow is what's giving me an error I just need a legend beside the plot to show what each colour stands for, but "legend" is not included as an argument of limma's volcanoplot...?

Dear Christopher,

I'm counting 8 opening but only 7 closing parentheses in your code snippet.

Cheers,

 - axel

Type

?legend

Legends are added to plots, not made during the plot.