[R] read table for Fisher Exact
David Winsemius
dwinsemius at comcast.net
Fri May 14 05:29:31 CEST 2010
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
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