Hi, I am obtaining an error when using coverageMat to compute the coverage matrix of the mouse LocusLink to GOCC mappings The error I obtain is: Error in mat(x) %*% mat(y) : matrices not conformable for multiplication I'm running ontoTools v1.2.1 on R 1.9.0 Dev for Windows. GO version is 1.5 and MouseLLMappings is 1.1.1 Code used to generate mappings was: mu.ll.tags <- ls(env=mouseLLMappingsLL2GO) mu.ll2goCC.Env <- new.env(hash=TRUE) mu.kvmap.CC <- list() #do ll-goid extractions for mu-LL and CC cat(length(mu.ll.tags )) for (i in 1:length(mu.ll.tags )) { if (i%%200 == 0) cat(i) tmp <- get(mu.ll.tags[i], env = mouseLLMappingsLL2GO) #extract GO-ids for current LL id tmp <- tmp[tmp %in% GOCCtags] #find those GO-ids that occur in Molecular Function only if (length(tmp) > 0) { mu.kvmap.CC[[mu.ll.tags[i]]] <- tmp assign(mu.ll.tags[i], tmp, env = mu.ll2goCC.Env) } } #unique LL and GO id's are species and sub-ontology specific, so use the following gotargs.mu.CC <- sortuniqueunlistmu.kvmap.CC))) llused.mu.CC <- namesmu.kvmap.CC) #generate mapping object mu.LL2GOCC.ooMap.1.5 <- otkvEnv2namedSparsellused.mu.CC, gotargs.mu.CC , mu.ll2goCC.Env) #generate object-ontology complex mu.LL2GOCC.ooc1.5 <- new("OOC", ontology=GOCC1.5, OOmap=mu.LL2GOCC.ooMap.1.5) covMat.mu.LL2GOCC.ooc1.5 <- coverageMat(mu.LL2GOCC.ooc1.5) 25050075010001250Error in mat(x) %*% mat(y) : matrices not conformable for multiplication The error is always occuring after the 1250 LocusLink block count Any help in solving this would be most appreciated. Best, Rohan Williams