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 <gwan...@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 <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. >> >> >> >> >> > >> > > [[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. -- 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 ______________________________________________ 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.
