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@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@ncsu.edu>
> To: arun <smartpink111@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@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@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<http://www.r-project.org/posting-guide.html>
> >and provide commented, minimal, self-contained, reproducible code.
> >
> >
>

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