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 ?cole Polytechnique F?d?rale de Lausanne (EPFL) Institut de math?matiques B?timent MA, Station 8 Tel: +41 21 693 2552 CH-1015 Lausanne Fax: +41 21 693 4303 SWITZERLAND

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 > ?cole Polytechnique F?d?rale de Lausanne (EPFL) > Institut de math?matiques > B?timent MA, Station 8 Tel: +41 21 693 2552 > CH-1015 Lausanne Fax: +41 21 693 4303 > SWITZERLAND > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > ------------------------------------------------------------ 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

At 08:00 PM 6/05/2006, bioconductor-request at stat.math.ethz.ch wrote: >Date: Fri, 5 May 2006 11:42:22 -0400 >From: Richard Friedman <friedman at="" cancercenter.columbia.edu=""> >Subject: Re: [BioC] base of B-value log in Limma - still not sure >To: Morten Mattingsdal <morten.mattingsdal at="" student.uib.no=""> >Cc: "bioconductor at stat.math.ethz.ch List'" > <bioconductor at="" stat.math.ethz.ch=""> > >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 The answer to this question is in Section 10.1 ("Output from eBayes") of the Limma User's Guide, where it is explained explicitly how to convert from the B-statistics into probabilities. In R and in mathematics, log() always means base-e unless otherwise stated. Other disciplines may be less precise, but all math stat journals that I know of follow this convention. The use of base-2 for M-values is a reference to 2-fold-changes, which have a traditional meaning. There is no such interpretation for probabilities or odds-ratios, hence no reason to use base-2 for the B-statistics. In any case, the B-statistic was defined by Lonnstedt and Speed (2002), and it is not appropriate for limma to change the definition. Best wishes Gordon