The table simply gives you the slope from a linear regression of the 3' - 5' ordered means, as well as a p-value from a test of the null hypothesis that the slope = 0. See ?AffyRNAdeg for a more in-depth explanation. In my experience, the plot (plotAffyRNAdeg) is good for finding 'bad' chips; I simply look for chips that have a significantly different slope than the rest of the chips. By significant, I mean that 'eyeballometrically' it seems quite different. The density plot (resulting from a call to hist()) is also good for finding outlier chips. We have been having a bad run recently with high-background chips, and these always have a distribution that is much less right-skewed than the other chips, and is also shifted significantly to the right. Again, this is eyeballometric analysis. Any chip that has a significantly different shape and/or location than the other chips in a batch invariably shows up as an outlier (as determined by the residual plots you can do with affyPLM, and PCA on the expression values), so I routinely re-do chips that look bad on the density plot. Note here that location seems to be much more important than shape. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Richard Friedman <friedman@cancercenter.columbia.edu> 05/06/04 03:54PM >>> Dear Bioconductor Users, I am not clear on the meaning of the table that is output from the AffyRNAdeg and how to use it to find bad slides. I am also not clear on how to use the hist command to see if the data is as it should be. I would appreciate any pointers or literature references. 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/ "I'm giving up coffee. Now that it looks like I might top 6 feet, I don't want to risk spoiling it." - Isaac Friedman, age 14 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor