Robert G., I have tried to use the kOverA function to filter out genes for which there are no values greater than 3.8. However, I have found that genes are not selected which have values >3.8 (ie. 4.5) for 42 samples. I have version R2.2.0 and the updated Bioconductor package. library(genefilter) f1 <- kOverA(42, 3.8) selected <- genefilter(kidney_exp, f1) sum(selected) E <- as.matrix(kidney_exp[selected,]) rownames(E) <- kidney[selected,1] Can someone verify that this function is not working correctly? Thanks, Lana Schaffer Biostatistics/Informatics The Scripps Research Institute DNA Array Core Facility La Jolla, CA 92037 (858) 784-2263 schaffer at scripps.edu