Dear all, I have normalized two technical replicates (same RNA) with marray. After normalization, should a scatter plot of one array against another yield a slope of 1? I get a slope of about .5. Does this mean that I am either something is wrong with the program, or I am doing something wrong? I have tried the following normalizations: 1. normp <-maNorm(raw, norm="p") 2. normg<-maNormScale(normp, norm ="g") In each case the scatter plot yields a slope of .5 rather than 1. Any suggestions would be appreciated. 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@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "Little Lulu, Reads Cthulu". -Rose Friedman, Age 8

Hi Richard, I assume you have two technical replicate arrays and you are preforming a scatter plot between two normalized M values. Typically, you should not expect a correlation of 1 and you don't want to. The amount of correlation between replicate samples M values usually depends on the number the DE genes. If you have very small number of DE genes you would prefer to see very low correlation between M values. As most of the data represents white noise. However, if you have a large percentage of DE genes, then those values will drive the correlation between replicate M values and you will observe a higher correlation. Cheers Jean On Tue, 10 Aug 2004, Richard Friedman wrote: > Dear all, > > I have normalized two technical replicates > (same RNA) with marray. After normalization, > should a scatter plot of one array against another > yield a slope of 1? > I get a slope of about .5. > Does this mean that I am either something is wrong with the program, > or I am doing something wrong? > I have tried the following normalizations: > > 1. normp <-maNorm(raw, norm="p") > 2. normg<-maNormScale(normp, norm ="g") > > In each case the scatter plot yields a slope of .5 rather > than 1. > > Any suggestions would be appreciated. > > 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@cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > "Little Lulu, > Reads Cthulu". > -Rose Friedman, Age 8 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >