Question: RankProd: Why are p-values=0?
gravatar for brilladine
3.8 years ago by
United States
brilladine0 wrote:


I am trying to make a volcano plot using the outputs provided by RankProd. Many of my genes have a p-value = 0, according to RankProd, which makes plotting the -log10(p-value) difficult to plot. 

Are p-values = 0 the product of an error, or an underflow issue? What's the best way to address such underflow issues?


Thank you.

rankprod p-value • 1.3k views
ADD COMMENTlink modified 3.8 years ago by James W. MacDonald49k • written 3.8 years ago by brilladine0
Answer: RankProd: Why are p-values=0?
gravatar for James W. MacDonald
3.8 years ago by
United States
James W. MacDonald49k wrote:

I don't think it's an underflow issue. Instead, the p-values appear to be computed as

# permutations more extreme than observed/# permutations

And if you don't have any permuted statistics that are as or more extreme than your observed statistic, this ends up being

0/# permutations

There are arguments for doing something like

# permutations more extreme + 1 / # permutations

Which is what the limma package does, where you always count the observed result as one of the permuted observations. With 1000 permutations, it's a difference between 0 and 0.001, which is probably the basis of the argument - neither one is likely to be correct (the observed statistic is only expected to be part of the null distribution if there truly are no differences), but 0.001 is probably a bit more interpretable than a p == 0, so there you go.

ADD COMMENTlink written 3.8 years ago by James W. MacDonald49k

Also, a related paper by B. Phipson and G. Smyth (Stat Appl Genet Mol Biol. 2010): Permutation P-values should never be zero: calculating exact P-values when permutations are randomly drawn

ADD REPLYlink written 3.8 years ago by Diego Diez730
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 160 users visited in the last hour