[BioC] Help: LIMMA-decideTests and lfc option

[Sherosha Raj]

Hello everyone

I am unsure how to interpret the lfc option in the multiple testing
algorithm decideTests:
decideTests(object,method="separate",adjust.method="BH",p.value=0.05,lfc=0)

The explanation given is:
"If lfc>0 then contrasts are judged significant only when the
log2-fold change is at least this large in absolute value. For
example, one might choose lfc=log2(1.5) to restrict to 50% changes or
lfc=1 for 2-fold changes. In this case, contrasts must satisfy both
the p-value and the fold-change cutoff to be judged significant."

What is meant exactly? Is it within a particular contrast that the
log2FC>0 for a particular probeset? Or is it comparing across all the
contrasts specified?

If some one could offer a clarification  I would be most grateful.
Thank you.

-- 
Regards,
Sherosha

-- 
Regards,
Sherosha