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I have two vectors (a and b), which are each a sample of n = 10000 from the poisson distribution with lambda = 10.

x <- data.frame("a" = rpois(10000,1000), "b" = rpois(10000,1000))

I conduct 10000 two-sample poisson tests between each element of a and the corresponding element of b, where the null hypothesis is that the two numbers are from the same poisson distribution (the rate ratio is 1).

x$p.value <- NA
for (i in 1:nrow(x)) {
  temp <- poisson.test(c(x[i, "a"], x[i, "b"]), T = c(1,1), alternative = "two.sided")
  x$p.value[i] <- temp$p.value }

As the null hypothesis is obviously true for this simulated data, I would expect the 10000 resulting p-values to be evenly distributed between 0 and 1. However, this is not the case. Instead the histogram shows a significant rightward skew towards 1.

hist(x$p.value, breaks = seq(0,1, by = 0.01))

enter image description here

Why is this the case?

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    $\begingroup$ You are not reading the histogram correctly. By definition, histograms represent probability by means of area, not height. Look closely at the right hand side and notice that the high bars are balanced by neighboring low bars, producing a very uniform density across the board. This phenomenon (of bar heights bouncing around) is aliasing in the binning process, as discussed at stats.stackexchange.com/questions/401692/…. Use a uniform probability plot instead. $\endgroup$ – whuber May 16 '19 at 12:28
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    $\begingroup$ Thanks for the clarification and relevant links, this has solved the problem for me! $\endgroup$ – GenomeGnome May 17 '19 at 9:38

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