[BioC] estimation of number of False positive in limma

[Jenny Drnevich]

Hi Greg,

This topic has been answered on the list before... but the quick answer is: 
What adjusted p-value cutoff did you use to select the DEGs? This is your 
proportion of false positives in the DEG list.

Cheers,
Jenny


At 03:36 PM 5/4/2006, gregory voisin wrote:
>Hi Bioconductorians,
>
>   For my analyse , I use Limma in affylmGui... ( very practical).
>   After to see the documentation about B , pvalues, M, A ...I 
> selectionnned my interesting DEG ( Differential Expressed Genes)... but I 
> have always the same questions: how many False Positif have I in my list 
> of genes?Is it possible to estimate this proportion ?
>   I know ( I believe ) that the usage of FDR in Limma's procedure 
> adjusted only the p-value, and it's not available as in SAM analysis to 
> estimate the proportion of FP..
>
>   I would like your opinion on the problem..
>   Thanks
>   Greg
>
>
>
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>VOISIN greg.
>Bioinformaticien.
>Centre de recherche du CHUM.
>MONTREAL
>
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

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e-mail: drnevich at uiuc.edu