I don't think there is a boxplot command for an exprSet. You could try boxplot(as.data.frame(exprs(howard1.norm))) 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> 04/29/04 03:47PM >>> Dear Bioconductor users, I am currently running the latest version of affy 1.4.22 under R 1.9.0 on Mac OSX 10.3. I am able to get a boxplot on the unnormalized data but not on the normalized data. Here are excerpts from my session: > howard1.raw AffyBatch object size of arrays=640x640 features (67206 kb) cdf=MG_U74Av2 (12488 affyids) number of samples=21 number of genes=12488 annotation=mgu74av2 > howard1.norm <- rma(howard1.raw) > howard1.norm Expression Set (exprSet) with 12488 genes 21 samples phenoData object with 1 variables and 21 cases varLabels sample: arbitrary numbering > boxplot(howard1.raw) Yielded a boxplot. But > boxplot(howard1.norm) Error in boxplot.default(howard1.norm) : invalid first argument Question: Should the rma normalized file be displayed by boxplot with the commands that I have typed? If not: Is there a way to display a boxplot of the normalized file? If so: any suggestions. In addition to affy, I so far have the following packages installed in my Library: [bb01friedman1:~/Library/R/library] friedman% ls Biobase R.css affy affyPLM affycomp liblisting.Rda mgu74av2cdf reposTools Do I need anything else to run box plot on the normalized object? 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/ "'Chutes and Ladders' teaches cause and effect." - Rose Friedman, age 7