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**33k**• written 12.1 years ago by Richard Friedman •

**2.0k**

Question: base of B-value log in Limma

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Richard Friedman • **2.0k** 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
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Columbia University Medical Center
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"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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modified 11 months ago
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Gordon Smyth ♦ **33k**
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written
12.1 years ago by
Richard Friedman • **2.0k**

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Morten • **300** wrote:

Hi

From Replicated Microarray Data, Lonnsted & 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

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Gordon Smyth ♦ **33k**
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12.1 years ago by
Morten • **300**

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

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Gordon Smyth ♦ **33k**
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12.1 years ago by
Richard Friedman • **2.0k**

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
Institute for Cell & Molecular Biology Fax: +44 (0)131
6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
UK

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11 months ago by

Gordon Smyth ♦ **33k**

Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia

Gordon Smyth ♦ **33k** wrote:

The B-statistic is on the natural log scale (which means base e). In documenting, I followed the usual R practice that logs are always natural unless otherwise stated.

Lonnstedt and Speed (2002) used log10, but natural log is more usual for this sort of statistic in other fields of statistics.

There is no reason why logFC and B should use the same log base as they are quite different sort of quantities. The concept of doubling a log-odds quantity has no particular intuitive meaning whereas it does for a log-fold-change.

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