Hi everyone,
I would like to know if there is any statistical motivation to plot -log(p-value) vs log(FC); why not -log(FDR) vs log(FC) directly?!?

Thanks! !!

There is none as far as I know reading different papers and reports, you can actually see [here][1] which reports volcano plot with -log10(FDR) vs log2(FC), at the end of the day it depends upon the user to use the best scaling metrics for the most represented visualization.

According to the definition it is the plots significance versus fold-change on the y- and x-axes, respectively. So your significance can be FDR corrected as well and in that case you are just restricting your FC values to a much stricter subsets to give more confidence to the visualization. There should not be any other statistical motivation other than giving it a more reliable plotting with less error prone significant points.


  [1]: http://www.nature.com/articles/srep05698/figures/5