Missing 'Yes' and Color in my CummeRbund csVolcano

[jmwhitha]

Hello SeqAnswers community,

Does anyone know why my csVolcano plot is not showing 'Yes' under significant in the legend?

When I try the following, there is no change:
> png(file="csVolcano.png")
> csVolcano(genes(cuff_data_1),'S1','S2', showSignificant=TRUE)
> dev.off()

Yes, I am aware there is a cluster around y-axis value 4. From what I can tell, this is due to a minimum limit in p-value (0.0001) that's a default in CuffDiff. Loyal's trick (below) on http://seqanswers.com/forums/showthread.php?t=19278 didn't change the cluster problem.

v<-csVolcano(genes(cuff),'Sample_A','Sample_B')
v+ scale_y_continuous(limits = c(0, 20))

I'd appreciate any help.

Thanks and God bless,
Jason

[jmwhitha]

Actually figured this out!

Hello all,

I figured this one out. You need the alpha and showSignificant=T paramaters in the command.

Ex:
csVolcano(genes(cuff_data_1),'S1','S2', alpha=0.05, showSignificant=T)

Peace,
Jason