Dear Bioconductor users, If the marrayNorm command with the print-tip normalization option is used on a dye-reversed slide ira.norm <- maNorm(ira.raw, swirl=p) is the normalization done on each printip of each slide separately, or is print-tip reversal taken into account? That is to say, referring to the the paper (or technical report) "Normalizalization for cDNA Micorarray Data" by Yang, Dudoit, Luu, and Speed does the program normalize log(M) vs A or 1/2(M+M') vs 1/2(A+A') 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)