Hello everyone, I have a bit of code where I am using rpy2 to import R phyper so I can perform an hypergeometric test. Unfortunately our cluster does not have a functional installation of rpy2 working. So I am wondering if I could translate to scipy which would make the code completly independent of R. The python code I have is as following: def lphyper(self,q,m,n,k): """ self.phyper(self,q,m,n,k) Calculate p-value using R function phyper from rpy2 low-level interface. "R Documentation phyper(q, m, n, k, lower.tail = TRUE, log.p = FALSE) q: vector of quantiles representing the number of white balls drawn without replacement from an urn which contains both black and white balls. m: the number of white balls in the urn. n: the number of black balls in the urn. k: the number of balls drawn from the urn. log.p: logical; if TRUE, probabilities p are given as log(p). lower.tail: logical; if TRUE (default), probabilities are P[X <= x], otherwise, P[X > x]. """ phyper_q = SexpVector([q,], rinterface.INTSXP) phyper_m = SexpVector([m,], rinterface.INTSXP) phyper_n = SexpVector([n,], rinterface.INTSXP) phyper_k = SexpVector([k,], rinterface.INTSXP) return phyper(phyper_q,phyper_m,phyper_n,phyper_k,**myparams)[0] I have looked to scipy.stats.hypergeom but it is giving me a different result which is also negative.
1-phyper(45, 92, 7518, 1329) [1] 6.92113e-13
In [24]: stats.hypergeom.sf(45,(92+7518),92,1329) Out[24]: -8.4343643180773142e-12 This was supposed to be an error with an older version of scipy but I am using more recent versions of it which should not contain the error anymore: In [26]: numpy.__version__ Out[26]: '1.5.1' In [27]: scipy.__version__ Out[27]: '0.9.0' thank you very much in advance for any help. Best, Bruno