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

[Richard Friedman]

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


On May 4, 2006, at 2:16 AM, Morten Mattingsdal wrote:

> Hi
> From Replicated Microarray Data, Lönnsted & Speed it seems to be the 
> "natural" log with base 10. (Equation 3 in the paper.) I presume this 
> is implemented in Limma.
> There is no reason to belive the base is 2.
> HTH
> morten
>
> Richard Friedman wrote:
>> Dear Bioconductor users,
>>
>> 	I have been assuming that the base of the
>> B-value log in Limma = 2, but I recently reread the
>> paper and didn;t see a base. Is the base 2,
>> and if not what is it/
>>
>> Thanks and best wishes,
>> Rich
>> ------------------------------------------------------------
>> 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
>>
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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