[R] read table for Fisher Exact

[Shi, Tao]

Thanks, David!




----- Original Message ----
> From: David Winsemius <dwinsemius at comcast.net>
> To: Frank E Harrell Jr <f.harrell at vanderbilt.edu>
> Cc: "Shi, Tao" <shidaxia at yahoo.com>; r-help at r-project.org
> Sent: Thu, May 13, 2010 8:29:31 PM
> Subject: Re: [R] read table for Fisher Exact
> 
> 
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<
> ymailto="mailto:f.harrell at vanderbilt.edu" 
> href="mailto:f.harrell at vanderbilt.edu">f.harrell at vanderbilt.edu>
>>> 
> To: 
> href="mailto:r-help at r-project.org">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