RankProd: Why are p-values=0?
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brilladine • 0
@brilladine-8236
Last seen 6.3 years ago
United States

Hello,

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 • 1.7k views
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@james-w-macdonald-5106
Last seen 1 hour ago
United States

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.

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