RNA-Seq, volcano plot

[liuchenxi2004]

Hi all

I am an entomologist, with little background of bioinformatics. I just want to know how to make a Volcano plot (statistics) with RNA-Seq data.
Any guidance would be much appreciated
Thanks in advance

[jmwhitha]

You probably figured this out by now, but here's some commands if not. The "png..." and "dev.off()" command will save the image for you. Instead of CDS, you can use genes or isoforms, etc. Changing the alpha will dislay as more or less red dots corresponding to significant differentially expressed CDS, genes, etc. And, xlimits will help to widen or narrow you image; this may cause you to loose data points so try c(-20,20) or higher.

png(file="csVolcano.png")
csVolcano(CDS(cuff_data_1),'OTA14h1','WT14h1', alpha=0.05, showSignificant=T, xlimits = c(-5, 5)
)
dev.off()