As an additional but related question. Is it possible to change the proportion of falsely rejected hypotheses given using the Benjamini and Hocberg fdr procedures in multtest or the p.adjust/topTable functions in limma. I suspect that 0.05 is also too conservative -----Original Message----- From: Stephen Henderson To: 'bioconductor@stat.math.ethz.ch' Sent: 08/12/03 13:49 Subject: [BioC] Limma parameters I've been examining the eBayes function in Limma using some affymetrix data we have. The default proportion setting: 0.01 I think is probably wrong for the comparison of tissue groups I have. Is there a rational way to estimate/guesstimate the correct proportion? Or isn't that the point anyway? Stephen ********************************************************************** This email and any files transmitted with it are confidentia...{{dropped}} _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor ********************************************************************** This email and any files transmitted with it are confidentia...{{dropped}}

Stephen, I'm not sure that I understand the question. The default proportion in eBayes is not the false discovery rate, as you probably already know. You are free to select as many genes as you like your topTable from limma, going as far down into the higher false discovery rates as you like. Just change the 'number' parameter to ask for more genes. The Benjamini and Hochberg idea is that, wherever you stop, you have controlled the FDR at that level. (Note however that this makes assumptions which are not true for microarray data.) There is no 0.05 default in limma. Regards Gordon At 02:50 AM 9/12/2003, you wrote: >As an additional but related question. Is it possible to change the >proportion of falsely rejected hypotheses given using the Benjamini and >Hocberg fdr procedures in multtest or the p.adjust/topTable functions in >limma. > >I suspect that 0.05 is also too conservative > >-----Original Message----- >From: Stephen Henderson >To: 'bioconductor@stat.math.ethz.ch' >Sent: 08/12/03 13:49 >Subject: [BioC] Limma parameters > > I've been examining the eBayes function in Limma using some affymetrix >data >we have. The default proportion setting: 0.01 I think is probably wrong >for >the comparison of tissue groups I have. > >Is there a rational way to estimate/guesstimate the correct proportion? >Or >isn't that the point anyway? > >Stephen