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 <smartpink...@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 <gwan...@ncsu.edu>
> To: arun <smartpink...@yahoo.com>
> Cc: R help <r-help@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 <smartpink...@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 <gwan...@ncsu.edu>
> >To: arun <smartpink...@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 <smartpink...@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 <gwan...@ncsu.edu>
> >>To: r-help@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@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.
> >>
> >>
> >
>
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