[R] read table for Fisher Exact

[Frank E Harrell Jr]

On 05/13/2010 08:16 PM, Shi, Tao wrote:
> Hi Prof. Harrell,
>
> Could you please elaborate on why chi-square test is more appropriate in this case?  Thank you very much!
>
> ...Tao

Exact tests tend to not be very accurate.  Typically their P-values are 
too large.  See

@Article{cra08how,
   author = 		 {Crans, Gerald G. and Shuster, Jonathan J.},
   title = 		 {How conservative is {Fisher's} exact test? {A} 
quantitative evaluation of the two-sample comparative binomial trial},
   journal = 	 Statistics in Medicine,
   year = 		 2008,
   volume = 	 27,
   pages = 	 {3598-3611},
   annote = 	 {Fisher's exact test; $2\times 2$ contingency table;size 
of test; comparative binomial experiment;first paper to truly quantify 
the conservativeness of Fisher's test;``the test size of FET was less 
than 0.035 for nearly all sample sizes before 50 and did not approach 
0.05 even for sample sizes over 100.'';conservativeness of ``exact'' 
methods;see \emph{Stat in Med} \textbf{28}:173-179, 2009 for a criticism 
which was unanswered}
}


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> ----- Original Message ----
>> From: Frank E Harrell Jr<f.harrell at vanderbilt.edu>
>> To: r-help at r-project.org
>> Sent: Thu, May 13, 2010 5:35:07 AM
>> Subject: Re: [R] read table for Fisher Exact
>>
>> On 05/12/2010 03:31 PM, visser wrote:
>>
>> i have 2 groups i want to
>> compare: group A and group B
>> each group contains let's say 20
>> patients
>> i want to perform a Fisher Exact test on genotype
>> distribution
>> so, see if there is a sign diff in genotpe
>> frequency/distribution (#AA, #AB,
>> #BB) between group A and B
>> not
>> for 1, but for 1000 different genes
>>
>> my question: how should i
>> build my table so i can do:
>>
>> test<-
>> read.table("table1.txt")
>> fisher.test(test)
>>
>> i know a lot
>> is still missing in the syntax, but i do not know what. any
>> help would
>> be soo much appreciated!!
>
> Note that in this case, Fisher's exact test has
>> a good chance of being
> less accurate than an approximate Pearson chi-square
>> test.
>


-- 
Frank E Harrell Jr   Professor and Chairman        School of Medicine
                      Department of Biostatistics   Vanderbilt University