[BioC] Top 10% of genes based on p-value in TopTable

[Ovokeraye Achinike-Oduaran]

Hi all,

I'm curious to know how I can get and highlight the top 10% of the
genes based on p-values that I get from my limma analysis in a volcano
plot.

I can get the genes highlighted based on an absolute logFC >2 and a
p-value<0.01(code below) but I would like to have an idea of the
number of genes in the top 10% based simply on p-values.

Any help will be greatly appreciated.

Thanks.

-Avoks

results$threshold = as.factor(abs(results$logFC) > 2 & results$P.Value < 0.01)
windows()
pdf("VolcanoPlot_GSE25724_9.pdf");

g = ggplot(data=results, aes(x=logFC, y=-log10(P.Value), colour=threshold)) +
  geom_point(alpha=0.4, size=1.75) +
  opts(legend.position = "none") +
  xlim(c(-8, 8)) + ylim(c(0, 10)) +
  xlab("log2 fold change") + ylab("-log10 p-value")
g
dev.off()