[R] Fisher's Exact Test

[Peter Dalgaard BSA]

partha_bagchi at hgsi.com writes:

> Appology in advance if this has been asked and answered. I am getting different
> answers using Fisher's exact test in the package ctest. For example:
> x_cbind(c(8, 22), c(31, 29))
> fisher.test(x)
> 
>     Fisher's Exact Test for Count Data 
> 
> data:  x 
> p-value = 0.04024 
> alternative hypothesis: two.sided 
> 
> However, in SAS or other packages on the net the answer I get is p-value=
> 0.02664.
> 
> Is this a result of the Clarkson, Fan & Joe (1993) improvement or am I doing
> something fundamentally wrong?
> (the above is only an example - I get different (from R) answers when I use 
> different input matrices).

With the most recent ctest, I actually get

> fisher.test(x)

         Fisher's Exact Test for Count Data 

data:  x 
p-value = 0.02664 
alternative hypothesis: two.sided 

The confusion is caused by this:

> fisher.test(x,alt="l")

         Fisher's Exact Test for Count Data 

data:  x 
p-value = 0.02012 
alternative hypothesis: less 


So the old definition of the p-value is 2 * (one-sided p), whereas the
new one sums those point probabilities that are less than or equal to
the observed one. 

Mind you, there's a paper by Yates lying somewhere in my "must read
some time" stack where he argues that the 2 * p procedure is more
correct...

-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)             FAX: (+45) 35327907
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