That's what I do: library(goTools) data(probeID) ontoCompare(affylist, probeType="hgu133a", plot=TRUE) That's what I get: [1] "Starting ontoCompare..." Error in if (ncol(results) == 0) results <- NA : argument is of length zero goTools version 1.0.6 R version 2.1.0 BioC release 1.6 Gentoo Linux Thank you, Juerg Straubhaar UMass Med