[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.
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
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] ml-node+2197479-2091597772-257...@n4.nabble.com Date: Thursday, May 13, 2010 2:36 pm Subject: Re: read table for Fisher Exact To: visser s.m@amc.uva.nl 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) = -- View this message in context: http://r.789695.n4.nabble.com/read-table-for-Fisher-Exact-tp2196762p2197720.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ 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 f.harr...@vanderbilt.edu 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
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 Jrf.harr...@vanderbilt.edu
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
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 Jrf.harr...@vanderbilt.edu
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
Thanks, David!
- Original Message
From: David Winsemius dwinsem...@comcast.net
To: Frank E Harrell Jr f.harr...@vanderbilt.edu
Cc: Shi, Tao shida...@yahoo.com; 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.
