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 Abundance Ratio for every pentaplicate, 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 like normal Volcano plots.
Does anyone know how to effectively make Volcano plot by using Abundance ratio of proteins?
Thank you a lot!!!
I don't think it will be difficult. This is done simply by using GraphPad Prism.
You shouldn't use adjusted P-values.
And the horizontal axis should show log ratios (to whatever basis).
I don't see any reason why you should not use the result of t-tests. Just make sure that the log abundances are compared.
- Badges
- Science method