[R] Help for Fisher's exact test

Steve Lianoglou mailinglist.honeypot at gmail.com
Tue Jul 17 04:58:59 CEST 2012


Hi,

You can see how to perform a Fisher's exact test by looking at its
documentation:

R> ?fisher.test

Note that section 2.7 of the edgeRUsersGuide is entitled "What to do
if you have no replicates", which you might want to read through:

http://bioconductor.org/packages/2.10/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf

-steve

On Mon, Jul 16, 2012 at 9:06 PM, Guanfeng Wang <gwang11 at ncsu.edu> wrote:
> Hi, A.K,
>      Thank you so much for your help. I did use DEGseq for analyzing the
> RNA-seq data, but I am not confidence about it, because most papers using
> it have biological replicates, I did not. And it is a good idea to ask the
> author who has used Fisher exact test for publication. Thanks again.
>
> Best,
> Feng
>
> On Mon, Jul 16, 2012 at 8:42 AM, arun <smartpink111 at yahoo.com> wrote:
>
>>
>>
>> Hi Feng,
>>
>> Have you looked at "DEGseq" package?  The "DEGexp() has FET (Fisher exact
>> test) in its method option.  Also, if you have seen papers using Fisher
>> exact test in R, it would  be better to email them for the package they
>> used.  I tried fisher.test(), but it is returning errors.
>>
>>
>>
>>
>> A.K.
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ________________________________
>> From: Guanfeng Wang <gwang11 at ncsu.edu>
>> To: arun <smartpink111 at yahoo.com>
>> Cc: R help <r-help at r-project.org>
>> Sent: Monday, July 16, 2012 6:34 AM
>> Subject: Re: [R] Help for Fisher's exact test
>>
>>
>> Hi, A.K.,
>>     Thank you very much for your help. For the RNA-seq data, the values in
>> columns WT and mt are raw read data. I do not have biological replicate, so
>> it is not suitable for using edgeR for the analysis. Some papers used
>> Fisher's exact test in R package. I do not know whether the p-value from
>> "statmod" will suitable for publication, but I will try. Thank you very
>> much.
>>    Does anyone know how to use Fisher's exact test in R? Could you please
>> send me the script if can? Thanks.
>>
>> Best,
>> Feng
>>
>>
>> On Mon, Jul 16, 2012 at 12:11 AM, arun <smartpink111 at yahoo.com> wrote:
>>
>> Hello,
>> >
>> >I am trying to understand the columns WT and mt in the dataset.  Is it
>> the FPKM or RPKM normalized values?  For RNA-seq, I think there are
>> packages available in bioconductor like edgeR to calculate the fisher exact
>> test (?binomTest).  Here, I was able to get the p-values using another
>> package "statmod" sage.test().  It is kind of obsolete, but I don't have
>> edgeR installed in my system.  Anyway, according to this paper (
>> http://genomebiology.com/2010/11/3/R25/), sage.test calculates the Fisher
>> exact p-value for each gene (though it is originally designed for SAGE
>> analysis).
>> >
>> >
>> >#The code:
>> >###############################
>> >
>> >dat2<-read.csv("forstatisticanalysis.csv")
>> >dat3<-dat2[,2:3]
>> >library(statmod)
>> >apply(dat3,2,sum)
>> >  #   WT      mt
>> >#9783553 7423498
>> > dat4<-sage.test(dat3$WT,dat3$mt,n1=9783553,n2=7423498)
>> >dat5<-data.frame(dat2[,1:3],pvalue=dat4)
>> > head(dat5)
>> >#                           gname     WT     mt        pvalue
>> >#1                  GRMZM2G306345 585846 287928  0.000000e+00
>> >#2                  GRMZM2G353753 135154  88894 1.046979e-243
>> >#3 AC207722.2_FG009;GRMZM2G353753 135154  88894 1.046979e-243
>> >#4                  GRMZM2G084142 103986  99247  0.000000e+00
>> >#5    GRMZM2G083841;GRMZM2G084142 103986  99247  0.000000e+00
>> >#6                  GRMZM5G836166  90886 118740  0.000000e+00
>> >
>> > write.csv(dat5,file="Analyzeddata.csv")
>> >####################################################
>> >
>> >
>> >Hope this helps you.
>> >
>> >A.K.
>> >
>> >P.S: Please send your requests to R-help rather than to a single person.
>> It will get more responses.
>> >
>> >________________________________
>> >From: Guanfeng Wang <gwang11 at ncsu.edu>
>> >To: arun <smartpink111 at yahoo.com>
>> >Sent: Sunday, July 15, 2012 10:27 PM
>> >Subject: Re: [R] Help for Fisher's exact test
>> >
>> >
>> >
>> >Hi, A.K.,
>> >      Thank you very much for your reply. I have no much background of
>> statistic analysis. I attached some of my data, could you please help me to
>> take a look how to use Fishe's exact test in R for the analysis if you have
>> time? I want to know whether there is significant difference between WT and
>> mt of each  gene in column A by calculate the p-value.   I will appreciate
>> it very much if you can send me the script of the test in R.  Thank you
>> very much for your time.
>> >
>> >Best,
>> >Feng
>> >
>> >
>> >On Sun, Jul 15, 2012 at 1:28 PM, arun <smartpink111 at yahoo.com> wrote:
>> >
>> >Hi,
>> >>
>> >>These links might be useful for you:
>> >>
>> >>https://stat.ethz.ch/pipermail/r-help/2009-July/204926.html
>> >>
>> http://stat.ethz.ch/R-manual/R-patched/library/stats/html/fisher.test.html
>> >>
>> >>A.K.
>> >>
>> >>
>> >>
>> >>
>> >>----- Original Message -----
>> >>From: Guanfeng Wang <gwang11 at ncsu.edu>
>> >>To: r-help at r-project.org
>> >>Cc:
>> >>Sent: Saturday, July 14, 2012 5:05 PM
>> >>Subject: [R] Help for Fisher's exact test
>> >>
>> >>Hi, R-help,
>> >>    I have a group of data from RNA-seq want to be analyzed by  Fisher's
>> >>exact test in R. I want to compare the significant difference of about
>> >>30,0000 individuals in two different samples, and I have no idea how to
>> use
>> >>R, so could you  please give me some suggestions or the scripts for
>> >>Fisher's exact test? Thank you very much.
>> >>
>> >>Best,
>> >>Guanfeng Wang
>> >>
>> >>    [[alternative HTML version deleted]]
>> >>
>> >>______________________________________________
>> >>R-help at 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.
>> >>
>> >>
>> >
>>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
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> and provide commented, minimal, self-contained, reproducible code.



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact



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