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

[Richard Friedman]

Dear Darlene,

	Thank you very much!

Best wishes,
Rich

On May 5, 2006, at 3:52 PM, Darlene Goldstein wrote:

> 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
>
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------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
Lecturer
Department of Biomedical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University Medical Center
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/


"Cartesian duelism is when somebody told Decartes that he didn't think
therefore he was, and Descartes challenged him to a duel".
-Isaac Friedman, age 16