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 mtpvalue #1 GRMZM2G306345 585846 287928 0.00e+00 #2 GRMZM2G353753 135154 88894 1.046979e-243 #3 AC207722.2_FG009;GRMZM2G353753 135154 88894 1.046979e-243 #4 GRMZM2G084142 103986 99247 0.00e+00 #5GRMZM2G083841;GRMZM2G084142 103986 99247 0.00e+00 #6 GRMZM5G836166 90886 118740 0.00e+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, 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.htmlhttp://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.
Re: [R] Help for Fisher's exact test
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 mtpvalue #1 GRMZM2G306345 585846 287928 0.00e+00 #2 GRMZM2G353753 135154 88894 1.046979e-243 #3 AC207722.2_FG009;GRMZM2G353753 135154 88894 1.046979e-243 #4 GRMZM2G084142 103986 99247 0.00e+00 #5GRMZM2G083841;GRMZM2G084142 103986 99247 0.00e+00 #6 GRMZM5G836166 90886 118740 0.00e+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, 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
Re: [R] Help for Fisher's exact test
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 mtpvalue #1 GRMZM2G306345 585846 287928 0.00e+00 #2 GRMZM2G353753 135154 88894 1.046979e-243 #3 AC207722.2_FG009;GRMZM2G353753 135154 88894 1.046979e-243 #4 GRMZM2G084142 103986 99247 0.00e+00 #5GRMZM2G083841;GRMZM2G084142 103986 99247 0.00e+00 #6 GRMZM5G836166 90886 118740 0.00e+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, 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
[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, 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.
