Question: Volcano plot p-value or FDR?
5
gravatar for balestrieri.c
3.4 years ago by
Milan
balestrieri.c50 wrote:

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! !!

rna-seq • 6.7k views
ADD COMMENTlink modified 3.4 years ago by ivivek_ngs4.8k • written 3.4 years ago by balestrieri.c50

It's always a good practice to use corrected p-values instead of p-values.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Nicolas Rosewick8.1k
3
gravatar for ivivek_ngs
3.4 years ago by
ivivek_ngs4.8k
Seattle,WA, USA
ivivek_ngs4.8k wrote:

There is none as far as I know reading different papers and reports, you can actually see here 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.

ADD COMMENTlink written 3.4 years ago by ivivek_ngs4.8k
4
gravatar for Benn
3.4 years ago by
Benn7.7k
Netherlands
Benn7.7k wrote:

I always use FDR corrected p-values, also in volcanoplots.

In these plots I use -log10(adjusted p-value) and the log2(FC).

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Benn7.7k
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