[BioC] Limma parameters and FDR
smyth at wehi.edu.au
Tue Dec 9 00:29:59 MET 2003
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.
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
>I suspect that 0.05 is also too conservative
>From: Stephen Henderson
>To: 'bioconductor at 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
>we have. The default proportion setting: 0.01 I think is probably wrong
>the comparison of tissue groups I have.
>Is there a rational way to estimate/guesstimate the correct proportion?
>isn't that the point anyway?
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