[R] fisher exact vs. simulated chi-square

Thomas Lumley tlumley at u.washington.edu
Wed Apr 23 16:44:04 CEST 2003

On Wed, 23 Apr 2003, Bob Porter wrote:

> The Chi-Square test is based upon the assumption that the sample is large enough
> to allow approximation of a (nearly symetric) binomial by a normal distribution.
> (Chi Sqare is z^2).  When expected (NOT observed) cells are too small, that
> suggests a very asymetric binomial and, consequently a poor fit for the
> assumption.  The exact test calculates the exact probability of the observed
> values, or more extreme ones, given the assumed probabilities generating the
> expected values.  As someone else noted, exact is exact, Chi-square is not
> (unless, of course, assumptions are exactly met.)

This is true but not the issue.  The question was about the difference
between the Fisher p.value and a Monte Carlo estimate of the exact p value
for the chisquared statisic.


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