Dear All, Just a note to alert others who might be getting unexpected results when using boxplot. If you type something like: boxplot(data$M ~ col(data$M)) any row (gene or spot) that has one or more missing values is not shown in the boxplot. In other words, the boxplots will only show the data for those rows (those genes or spots) that have no missing values over all the arrays. You do not get this behavior (i.e., you get all the points with data to be represented for each array) if you either: a) use a data frame: boxplot(as.data.frame(data$M)) b) set "options(na.action = "na.pass")" See my (unjustified) bug-report and B.D. Ripley's answer at http://r-bugs.biostat.ku.dk/cgi- bin/R/incoming?id=6846;user=guest;selectid=6846 Best, R. -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://bioinfo.cnio.es/~rdiaz PGP KeyID: 0xE89B3462 (http://bioinfo.cnio.es/~rdiaz/0xE89B3462.asc)