[R] hypergeometric vs fisher.test

[peter dalgaard]

On Aug 13, 2010, at 3:47 PM, Andrea Franceschini wrote:

> 
> Dear R team,
> I have a simple question.
> 
> I tried this command:
> phyper(17,449,19551,181, FALSE)
> [1] 1.47295e-07
> 
> and then I tried this command:
> (fisher.test(matrix(c(17,449,181,19551),2,2),
> alternative='greater'))$p.value
> [1] 3.693347e-06
> 
> 
> Shouldn't be identical the results of the two commands ?
> What is the difference ?

Just read the phyper docs more carefully (and perhaps revisit the theory), and you'll see that phyper is using margin totals of the table, where fisher.test is using the individual entries. Also beware of left/right continuity issues with tails of discrete distributions: The convention is that the lower and the upper tail sums to 1, so your "17" is NOT included in the upper tail.

> 
> Thx a lot
> -- 
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> 
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-- 
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com