[R] read table for Fisher Exact

[David Winsemius]

On May 13, 2010, at 9:24 PM, Frank E Harrell Jr wrote:

> 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}
> }
>

Lest you be concerned that Frank is selectively citing the literature,  
here are a few more citations demonstrating problems with "exact  
methods", starting with the citation in the prop.test help page:

http://www.stats.org.uk/statistical-inference/Newcombe1998.pdf

And a few others:

http://www.jstor.org/pss/2685469
http://www.ine.pt/revstat/pdf/rs080204.pdf
http://goliath.ecnext.com/coms2/gi_0199-4388181/Evaluation-criteria-for-discrete-confidence.html
http://www.math.ist.utl.pt/~apires/PDFs/AP_COMPSTAT02.pdf

Some R methods:

http://finzi.psych.upenn.edu/R/library/PropCIs/html/add4ci.html
http://finzi.psych.upenn.edu/R/library/pairwiseCI/html/pairwiseCImethodsProp.html
http://finzi.psych.upenn.edu/R/library/Epi/html/ci.pd.html
http://finzi.psych.upenn.edu/R/library/binMto/html/binMtoMethods.html
http://finzi.psych.upenn.edu/R/library/pairwiseCI/html/pairwiseCI.html




>>
>>
>>
>>
>>
>> ----- 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
>
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David Winsemius, MD
West Hartford, CT