Question: how to combine p values?
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gravatar for Reema Singh
8.9 years ago by
Reema Singh570
Reema Singh570 wrote:
Hi All I want to combine the two datasets using p-values. Can anybody tell me how to combine p values from two different datasets using R? It would be a great help Waiting for reply.... REGARDS~ Reema Singh [[alternative HTML version deleted]]
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ADD COMMENTlink modified 8.9 years ago by Moshe Olshansky120 • written 8.9 years ago by Reema Singh570
Answer: how to combine p values?
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gravatar for Moshe Olshansky
8.9 years ago by
Moshe Olshansky120 wrote:
Hi Reema, there are several ways to do so (you can search the Internet). I am not sure whether there exists a really good one. One possibility is as below: let P1 and P2 be the p-values from dataset 1 and dataset 2. Under the null hypothesis both p-values are distributed uniformly in [0,1]. If we assume independence then the probability that their product is less than x equals x - x*log(x) (where log is the natural - base e - logarithm). So your combined p-value is P1*P2 - P1*P2*log(P1*P2). Best regards, Moshe. --- On Thu, 9/12/10, Reema Singh <reema28sep at="" gmail.com=""> wrote: > From: Reema Singh <reema28sep at="" gmail.com=""> > Subject: [BioC] how to combine p values? > To: bioconductor at r-project.org > Received: Thursday, 9 December, 2010, 8:50 PM > Hi All > > I want to combine the two datasets using p-values. > Can anybody tell me how to combine p values from two > different datasets > using R? > > It would be a great help > > Waiting for reply.... > > REGARDS~ > Reema Singh > > ??? [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 8.9 years ago by Moshe Olshansky120
There are several methods to combine p-values. Fisher method, Z-transform method (also called Stouffer method), etc.The paper below explains the methods. Whitlock, M. C. (2005) "Combining probability from independent tests: the weighted Z-method is superior to Fisher’s approach", J. Evol. Biol., 18, pages 1368–1373. You can download the package called "survcomp" ( http://cran.r-project.org/web/packages/survcomp/). This package contains Fisher method using "combine.test" routine. You can also refer the following paper for methods: http://statgen.ncsu.edu/zaykin/tpm/tpmfinal.pdf Good luck, ~Nikhil On Thu, Dec 9, 2010 at 6:37 PM, Moshe Olshansky <m_olshansky@yahoo.com>wrote: > Hi Reema, > > there are several ways to do so (you can search the Internet). I am not > sure whether there exists a really good one. > One possibility is as below: > let P1 and P2 be the p-values from dataset 1 and dataset 2. Under the null > hypothesis both p-values are distributed uniformly in [0,1]. If we assume > independence then the probability that their product is less than x equals x > - x*log(x) (where log is the natural - base e - logarithm). So your combined > p-value is P1*P2 - P1*P2*log(P1*P2). > > Best regards, > Moshe. > > --- On Thu, 9/12/10, Reema Singh <reema28sep@gmail.com> wrote: > > > From: Reema Singh <reema28sep@gmail.com> > > Subject: [BioC] how to combine p values? > > To: bioconductor@r-project.org > > Received: Thursday, 9 December, 2010, 8:50 PM > > Hi All > > > > I want to combine the two datasets using p-values. > > Can anybody tell me how to combine p values from two > > different datasets > > using R? > > > > It would be a great help > > > > Waiting for reply.... > > > > REGARDS~ > > Reema Singh > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 8.9 years ago by Nikhil Garge20
Thank you for references, Paul and Nikhil! --- On Fri, 10/12/10, Nikhil Garge <nikhil.garge@gmail.com> wrote: From: Nikhil Garge <nikhil.garge@gmail.com> Subject: Re: [BioC] how to combine p values? To: "Moshe Olshansky" <m_olshansky@yahoo.com>, bioconductor@r-project.org, "Reema Singh" <reema28sep@gmail.com> Received: Friday, 10 December, 2010, 12:25 PM There are several methods to combine p-values. Fisher method, Z-transform method (also called Stouffer method), etc.The paper below explains the methods. Whitlock, M. C. (2005) "Combining probability from independent tests: the weighted Z-method is superior to Fisher’s approach", J. Evol. Biol., 18, pages 1368–1373. You can download the package called "survcomp" (http://cran.r-project.org/web/packages/survcomp/). This package contains Fisher method using "combine.test" routine. You can also refer the following paper for methods: http://statgen.ncsu.edu/zaykin/tpm/tpmfinal.pdf Good luck,~Nikhil On Thu, Dec 9, 2010 at 6:37 PM, Moshe Olshansky <m_olshansky@yahoo.com> wrote: Hi Reema, there are several ways to do so (you can search the Internet). I am not sure whether there exists a really good one. One possibility is as below: let P1 and P2 be the p-values from dataset 1 and dataset 2. Under the null hypothesis both p-values are distributed uniformly in [0,1]. If we assume independence then the probability that their product is less than x equals x - x*log(x) (where log is the natural - base e - logarithm). So your combined p-value is P1*P2 - P1*P2*log(P1*P2). Best regards, Moshe. --- On Thu, 9/12/10, Reema Singh <reema28sep@gmail.com> wrote: > From: Reema Singh <reema28sep@gmail.com> > Subject: [BioC] how to combine p values? > To: bioconductor@r-project.org > Received: Thursday, 9 December, 2010, 8:50 PM > Hi All > > I want to combine the two datasets using p-values. > Can anybody tell me how to combine p values from two > different datasets > using R? > > It would be a great help > > Waiting for reply.... > > REGARDS~ > Reema Singh > >     [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD REPLYlink written 8.9 years ago by Moshe Olshansky120
I found, A systematic comparison of methods for combining p-values from independent tests , Thomas M. Loughin, Computational Statistics & Data Analysis 47 (2004) 467 – 485 a useful paper. I have used some of the methods in there with exon arrays If you enquiring about Meta analysis there is an R program called GeneMeta, and a another called "metal" (perl program I think). Metal is used for GWAS typically. Cheers Paul -----Original Message----- From: Moshe Olshansky <m_olshansky@yahoo.com> To: bioconductor@r-project.org, Reema Singh <reema28sep@gmail.com> Subject: Re: [BioC] how to combine p values? Date: Thu, 9 Dec 2010 15:37:03 -0800 Hi Reema, there are several ways to do so (you can search the Internet). I am not sure whether there exists a really good one. One possibility is as below: let P1 and P2 be the p-values from dataset 1 and dataset 2. Under the null hypothesis both p-values are distributed uniformly in [0,1]. If we assume independence then the probability that their product is less than x equals x - x*log(x) (where log is the natural - base e - logarithm). So your combined p-value is P1*P2 - P1*P2*log(P1*P2). Best regards, Moshe. --- On Thu, 9/12/10, Reema Singh <reema28sep@gmail.com> wrote: > From: Reema Singh <reema28sep@gmail.com> > Subject: [BioC] how to combine p values? > To: bioconductor@r-project.org > Received: Thursday, 9 December, 2010, 8:50 PM > Hi All > > I want to combine the two datasets using p-values. > Can anybody tell me how to combine p values from two > different datasets > using R? > > It would be a great help > > Waiting for reply.... > > REGARDS~ > Reema Singh > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD REPLYlink written 8.9 years ago by Paul Leo970
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