[BioC] (adj.p.value & log2FC) or (B.value & log2FC)

deb [guest] guest at bioconductor.org
Mon Dec 2 19:15:53 CET 2013

Hi Sir,
I have a simple question regarding cut-off parameter to be used for filtering out DEGs from the topT object obtained using LIMMA.
Which statistics is preferred more and why?
1) filter of adj.p.value and log2FC.
2) filter of B.value and log2FC.
I mean both give similar ranking of genes but usually I have  seen people using an adj.p.value cut-off of 0.01. What is the minimum cut-off value for B.value?(Is it 4?)
It is a technical question so I do not have any output to be put in the next sessionInfo() field.
Thank you for your input Sir.

 -- output of sessionInfo(): 

topT<- topTable(fit3, coef=1, adjust="BH", sort.by="B",number=nrow(data))

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