Hello, everyone!
I got a very weird shape of volcano plot with R. It doesn't have a typical shape and I want to figure out the reasons behind this problem.
In my plot, I found there were some some long gaps inside the Volcano plot without any dots. It seems that the data was not continuous.
However, I checked adjust p values ,they were continuous.
I couldn't understand how these gaps generated. I am sure the R code is correct.
I am wondering that it might be some thing wrong with my data processing. But I have no hint where this problem came from.
Any suggestions are welcomed!
Thank you in advance!
if some points were removed during plotting, R would report it I guess.. if no warning, maybe you could check whether there are any "-log10(p-value)"s falling into the gap value range (seems between 2.2-2.3)? And check your "p-value" class.
It's a bit strange to plot adjusted p-values in a volcanoplot... but that's a different topic.
Please use a logarithmic y-axis or log adj.P in your second plot to make them more comparable. Otherwise the gaps you see in the vocanoplot won't be visible in the lower plot.