Re: [R] read table for Fisher Exact
Thanks, David!
- Original Message
> From: David Winsemius
> To: Frank E Harrell Jr
> Cc: "Shi, Tao" ; r-help@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.harr...@vanderbilt.edu";
> href="mailto:f.harr...@vanderbilt.edu";>f.harr...@vanderbilt.edu>
>>>
> To:
> href="mailto:r-help@r-project.org";>r-help@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
> ChairmanSchool of Medicine
>
> Department of
> Biostatistics Vanderbilt University
>
>
> __
>
> ymailto="mailto:R-help@r-project.org";
> href="mailto:R-help@r-project.org";>R-help@r-project.org mailing list
>
>
> >https://stat.ethz.ch/mailman/listinfo/r-help
> 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
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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
To: r-help@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 ChairmanSchool of Medicine
Department of Biostatistics Vanderbilt
University
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
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
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] read table for Fisher Exact
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}
}
- Original Message
From: Frank E Harrell Jr
To: r-help@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 ChairmanSchool of Medicine
Department of Biostatistics Vanderbilt University
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] read table for Fisher Exact
Hi Prof. Harrell,
Could you please elaborate on why chi-square test is more appropriate in this
case? Thank you very much!
...Tao
- Original Message
> From: Frank E Harrell Jr
> To: r-help@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
__
> ymailto="mailto:R-help@r-project.org";
> href="mailto:R-help@r-project.org";>R-help@r-project.org mailing list
> href="https://stat.ethz.ch/mailman/listinfo/r-help"; target=_blank
> >https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting
> guide http://www.R-project.org/posting-guide.html
and provide commented,
> minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] read table for Fisher Exact
How much would that differ? And how should I build my table if I want to do a
Pearson Chi Sqaure?
- Original Message -
From: "Frank E Harrell Jr [via R]"
Date: Thursday, May 13, 2010 2:36 pm
Subject: Re: read table for Fisher Exact
To: visser
> 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 ChairmanSchool of Medicine
> Department of Biostatistics Vanderbilt University
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
> __
> View message @
> http://r.789695.n4.nabble.com/read-table-for-Fisher-Exact-tp2196762p2197479.html
>
> To unsubscribe from read table for Fisher Exact, click (link removed) =
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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 ChairmanSchool of Medicine
Department of Biostatistics Vanderbilt University
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] read table for Fisher Exact
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!!
--
View this message in context:
http://r.789695.n4.nabble.com/read-table-for-Fisher-Exact-tp2196762p2196762.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
