Does anyone know how to make normal volcano plot from Abundance ratio of proteins?
I have got Abundance Ratio for treatment (pentaplicates) and control (pentaplicates). Then, I obtained from machine something like mean Abundance Ratio, its division treatment/control Abundance Ratio and Adjusted P-value for treatment/control.
I wanted to make Volcano plot from Abundance Ratio and -Log10 of Adjusted P-value. I end up with strange Volcano plot. It is because Abundance ratio is never in minus values. So I made Log2 of Abundance Ratio, but the graphic looks even worse.
I also calculated Log2FC and P-value via t-test from all pentaplicates, but one scientist told me, that I cannot use it, even though the graphics by this calculation looks normal.
Does anyone know how to effectively make Volcano plot by using Abundance ratio?
Thank you a lot!!!