[BioC] [Limma] Using P value or B statistics for cutoff?

[Wu, Xiwei]

Hi, 

I am using Limma to analyze my data, which is a simple two-group comparison
(treated vs. control). The analysis is very straigtforward, but it becomes
not as easy when the gene list is to be generated. I noticed that some genes
with small P values (<0.05 adjusted with FDR) have negative B logodd scores,
which mean the chance of DE is <50%. For situation like this, should I use
log odd for cutoff or shoule I use P value or combined?

Xiwei Wu

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