Dear Bioconductor List, In an earlier posting, Gordon Smyth recommended a tentative cutoff of B>=0 for Limma output. Is it okay to publish Venn diagrams based on this cutoff or should the cutoff be validated by spot-checking with PCR? Is it okay to publish pathway overrepresentation analyses with this cutoff, or is PCR validation of the cutoff advised? 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 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