Binomial p-values for comparing pyrosequencing samples

Regarding my work on 454 pyrosequencing error rates with Professor Holmes this summer, I was recently asked about how to calculate a p-value for comparing two draws from a Binomial distribution to test the hypothesis that the number of substitutions seen in the sample is significantly greater than the number of substitutions seen in the control. There is actually no need to use the Poisson approximation, and the Binomial distribution very naturally takes care of varying coverage. I explain my approach here.

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