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]]

>

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