[BioC] estimation of number of False positive in limma
Jenny Drnevich
drnevich at uiuc.edu
Thu May 4 22:50:43 CEST 2006
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
330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA
ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu
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