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.
