Dear Bioconductor Users, Long time readers of this column realize that I have been experiencing some difficulty flattening the M vs A curve on my normalization. I have just tried applying 2 loess normalizations in a row with the default. That is to say I have done: ira.norm <- maNorm(ira.raw, norm = "p") ira.x2.norm <- maNorm(ira.norm, norm = "p") The curves flattened considerably. Is there a potenial problem with this procedure? 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/ "Spring, Summer, and Winter. Then Fall came along, and that's the end of our song, and the pigeons never hibernate at all". -Rose Friedman, age 7 (These are the correct lyrics and supersede the version previously at the end of my sig)