[BioC] base of B-value log in Limma - still not sure

[J.delasHeras at ed.ac.uk]

Quoting Richard Friedman <friedman at cancercenter.columbia.edu>:

> Dear Morten,
>
> 	Thank you for your answer, but I am still not sure based upon it.
> In Limma log2 is used for absolute intensities, and for  M.
> M=log2(Intenisity2)-log2(Intensity1). In limma, B and M appear in
> the same table and graphs. This is unusual if B and M have different
> bases.

Why is it unusual?

we use log2 for the ratios simply so that for each "unit" of M we 
double the ratio, as that seemed a reasonable scale. You could use log5 
if the scale of change justified it, for your purposes.

A while ago I was curious about the B value calculation and how the 
probabilities were translated into B, and I noticed that the log was 
definitely not in base 2. But I can't remember if it was base 10 or e...

If noone gives an answer I'll fish out my notes...

Jose

-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
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