[BioC] Limma FDR question

Ramon Diaz-Uriarte rdiaz at cnio.es
Fri Dec 10 14:00:31 CET 2004

Dear Manuel,

You are selecting the top-ranked number genes, ordered using the "sort.by" 
option; the p-value you are seeing is the fdr-adjusted p-value, so no, no 
pre-determined cut-off has been selected. Some explanation is provided in the 
help for p.adjust; here you also have an extensive list of references. You 
might want to add to that the documentation of the multtest package which 
provides a quick overview of multiple testing issues, including the 
definition of adjusted p-value according to FDR.



On Friday 10 December 2004 13:21, M PEREZ wrote:
> Hi all,
> I was wondering how the p-value correction using fdr works.
> The following Limma package’s command “ topTable(fit,number=100,
> adjust="fdr")” corrects the p-values but I don’t know which is the percent
> of false positive we can expect using  this correction. Is the FDR fixing
> at one pre-determined value, e.g.  5 %?
> Thank you in advance
> Best,
> Manuel
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Ramón Díaz-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

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