[BioC] Limma: how to obtain P values using method "global" for multiple testing

[Gordon K Smyth]

If fit is the fitted model object that you used for decidedTests(), then

   Global.Adjusted.P <- fit$p.value
   Global.Adjusted.P[] <- p.adjust(Global.Adjusted.P, method="BH")

Gordon


> Date: Sat, 21 Jul 2012 02:02:46 +0000
> From: "Ribeiro,Eduardo de Souza" <ribeiro.es at ufl.edu>
> To: "bioconductor at r-project.org" <bioconductor at r-project.org>
> Subject: [BioC] Limma: how to obtain P values using method "global"
> 	for multiple testing
>
> Hi everyone,
>
> I am analyzing a Affymetrix microarray data set using the Limma package. 
> According to my experimental design, I understand that my contrasts are 
> closely related and that I should use the "global" method for multiple 
> testing. My question is: Is there a way to obtain P-values using the 
> "global" method for multiple testing? The decideTest function allows to 
> specify the method "global" but just give the matrix of the results and 
> not the P-values. And if I understood correctly, the topTable function 
> does not allow to specify the method for multiple testing and uses the 
> "separate" method as default. Comparing the decideTest matrices, I 
> realize that the results of "separate" and "global" methods are slightly 
> different and I am concerned that this difference may change the final 
> interpretation of my study.
>
> Thank you very much.
>
> Best regards
>
> Eduardo Ribeiro
> PhD student
> University of Florida

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