[R] read table for Fisher Exact
Shi, Tao
shidaxia at yahoo.com
Fri May 14 06:46:41 CEST 2010
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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>
>
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> PLEASE do read the
> posting guide http://www.R-project.org/posting-guide.html
> and provide
> commented, minimal, self-contained, reproducible code.
David Winsemius,
> MD
West Hartford, CT
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