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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 > > > > * > * > ----------------- (o o)------------------- >-. .-. .-oOOo~(_)~oOOo-. .-. .-. >||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ >|/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X >' `-' `-' `-' `-' `-' `-' `-' >VOISIN greg. >Bioinformaticien. >Centre de recherche du CHUM. >MONTREAL > > > >--------------------------------- > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor 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