[BioC] Limma: genes with B<0

[Wu, Xiwei]

Dear Bioconductors,
 
I am wondering whether it makes sense to use genes with log odds less than 0
generated from Limma. There are only a handful of genes with B>0. I observe
the volcano plot of log odds vs. log ratios, and it seems to me that even
with B = -2, there is a pretty distinct group of genes that can be separated
from majority of other genes. However, if I understand it correctly, any
gene with B<0 has <50% probability to be differentially expressed. My
questions is what is the best way to choose the right B statistics, using
volcano plot as a guide or use arbitratry cutoffs like 0. Thanks,
 
Xiwei

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