[BioC] Limma parameters and FDR

[Stephen Henderson]

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 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
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 


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