I'm trying to do a very simple thing but my usual commands aren't working.
After fitting a bayesian fit to my model I wanted to do a volcano plot
fit <- eBayes(fit, trend=F)
#Get hits and plot
coef <- 3
hits <- topTable(fit, coef)
But I am unable to edit the volcano plot to add limits to the plot it produces.
I simply want to edit the x and y axis for their limits and highlight points anything above certain p-value level.
volcanoplot(fit, coef, ylim=c(-0.5, 25))
Error in volcanoplot(fit, coef, ylim = c(-0.5, 25)) :
unused argument (ylim = c(-0.5, 25))