Hi,

I just took the following code snippet from EdgeR tutorial to have volcano plot in my DEseq2 analysis workflow. I couldn't see interesting results. Is it because my lfc and pval threshold choice? Could someone please help?

tab = data.frame(logFC = res$log2FoldChange, negLogPval = -log10(res$pvalue))
head(tab)
par(mar = c(5, 4, 4, 4))
plot(tab, pch = 16, cex = 0.6, xlab = expression(log[2]~fold~change), ylab = expression(-log[10]~pvalue))
lfc = 2
pval = 0.01
signGenes = (abs(tab$logFC) > lfc & tab$negLogPval > -log10(pval))
points(tab[signGenes, ], pch = 16, cex = 0.8, col = "red") 
abline(h = -log10(pval), col = "green3", lty = 2) 
abline(v = c(-lfc, lfc), col = "blue", lty = 2) 
mtext(paste("pval =", pval), side = 4, at = -log10(pval), cex = 0.8, line = 0.5, las = 1) 
mtext(c(paste("-", lfc, "fold"), paste("+", lfc, "fold")), side = 3, at = c(-lfc, lfc), cex = 0.8, line = 0.5)

Thanks,

J.

Thanks Michael.