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
> -- 
> View this message in context: 
> http://r.789695.n4.nabble.com/hypergeometric-vs-fisher-test-tp2324223p2324223.html
> Sent from the R help mailing list archive at Nabble.com.
> 
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

-- 
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd....@cbs.dk  Priv: pda...@gmail.com

______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Reply via email to