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

[Darlene Goldstein]

Richard Friedman <friedman at ...> writes:

> 
> 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.
> 
> 	Also, at least in the usage with which I am familiar, "natural: logs 
> are
> base e not base 10" and I have seen "log" without a subscript used for
> both base 10 and base e logs. So even if B is not base 2 I am not
> usr eif it is base 10 or base e.
> 
> 	Would Gordon care to comment?
> 
> Thanks and best wishes,
> Rich

Hi, if you look at the code in eBayes.R, you will see that the B-stat is
computed with the R function 'log', and if you look at the documentation

?log

you will see that 'log' computes natural logarithms (where 'natural' 
means base e).

Best regards, Darlene

-- 
Darlene Goldstein
École Polytechnique Fédérale de Lausanne (EPFL)
Institut de mathématiques
Bâtiment MA, Station 8        Tel: +41 21 693 2552
CH-1015 Lausanne              Fax: +41 21 693 4303
SWITZERLAND