Hi all, Sorry to abuse the list with this general microarray question, but I was hoping someone could quickly help me out with this... why are M-values (log2(ratio of expression in A to B)) called M-values? Thanks, Jenny Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu

Jenny, If I am not mistaken, "M" stands for "Minus" and in log2(Exp)-Log2(Control). Similarly, "A" stands for "Add", as in 1/2[log2(Exp)+log2(control)]. The additional reference, is that "M" and "A" stand for "MicroArray". I am not sure who came up with this. I think the Speed group, but I am not sure who. Can anybodyelse help with this? Best wishes, Rich On Sep 29, 2006, at 2:29 PM, Jenny Drnevich wrote: > Hi all, > > Sorry to abuse the list with this general microarray question, but I > was > hoping someone could quickly help me out with this... why are M-values > (log2(ratio of expression in A to B)) called M-values? > > Thanks, > Jenny > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at uiuc.edu > > _______________________________________________ > 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/ "My novel has a hundred characters and it takes place over a year. When I finish it, if it is shorter than Ulysses, then Joyce described things too much". -Rose Friedman, age 9

Hi Jenny, Jenny Drnevich wrote: > Hi all, > > Sorry to abuse the list with this general microarray question, but I was > hoping someone could quickly help me out with this... why are M-values > (log2(ratio of expression in A to B)) called M-values? IIRC, it comes from MA plots, which are a plot of the log difference versus the log average (hence Minus vs Average ==> MvA plots). Ya list abuser ;-D Best, Jim > > Thanks, > Jenny > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at uiuc.edu > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

Hi Jenny, I believe they are called M-values because on a log scale, you are taking the difference (M for minus) of the intensity measurements in the two channels, i.e. log(Cy5/Cy3) = log(Cy5) - log(Cy3). Best, Debashis -- Debashis Ghosh Associate Professor of Biostatistics University of Michigan 1420 Washington Heights Ann Arbor, MI 48109-2029 email: ghoshd at umich.edu phone: (734) 615-9824 fax: (734) 763-2215 Quoting Jenny Drnevich <drnevich at="" uiuc.edu="">: > Hi all, > > Sorry to abuse the list with this general microarray question, but I was > hoping someone could quickly help me out with this... why are M-values > (log2(ratio of expression in A to B)) called M-values? > > Thanks, > Jenny > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at uiuc.edu > > _______________________________________________ > 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 > > >