I'm trying to calculate gene similarities for the yeast organism, but no matter which ontology or which term similarity I employ I get a lot of zeros in the gene similarity matrix. In fact the vast majority of the similarities turn out to be zero. Is this normal? I'm employing GOSim as in the following: library('org.Sc.sgd.db') library('GOSim') setEvidenceLevel(evidences = "all", organism=org.Sc.sgdORGANISM, gomap=org.Sc.sgdGO) setOntology(ont='MF') getGeneSim(as.character(labels),similarityTerm='Resnik') My vector named labels, contain gene names such as: YAL003W YAL004W YAL005C YAL008W YAL010C YAL011W YAL016W YAL018C. The result for such example are: YAL003W YAL005C YAL008W YAL010C YAL011W YAL016W YAL018C YAL003W 1.00000000 0.06968198 0 0 0 0.0588447 0 YAL005C 0.06968198 1.00000000 0 0 0 0.3116553 0 YAL008W 0.00000000 0.00000000 1 0 0 0.0000000 0 YAL010C 0.00000000 0.00000000 0 1 0 0.0000000 0 YAL011W 0.00000000 0.00000000 0 0 1 0.0000000 0 YAL016W 0.05884470 0.31165527 0 0 0 1.0000000 0 YAL018C 0.00000000 0.00000000 0 0 0 0.0000000 1 Is this amount of zeros normal? [[alternative HTML version deleted]]