Hi In my experience, the soap querying of KEGG has always been a bit flaky, whether using the perl modules or through the KEGGSOAP package. Eg > get.pathways.by.genes(c("eco:b0077", "eco:b0078")) Type: string & length = 4 [1] "path:eco00290" "path:eco00650" "path:eco00660" "path:eco00770" Warning messages: 1: Don't understand the SOAP type `string' yet in: fromSOAP(x, type = type, root = root, converters = converters, 2: Don't understand the SOAP type `string' yet in: fromSOAP(x, type = type, root = root, converters = converters, 3: Don't understand the SOAP type `string' yet in: fromSOAP(x, type = type, root = root, converters = converters, 4: Don't understand the SOAP type `string' yet in: fromSOAP(x, type = type, root = root, converters = converters, > get.pathways.by.genes(c("eco:b0077")) NULL > get.pathways.by.genes(c("eco:b0078")) NULL The same is true for salmonella: > query_vector[1:3] [1] "stm:STM4113" "stm:STM2974" "stm:STM0515" > get.pathways.by.genes(query_vector[1:2]) Type: string & length = 1 [1] "path:stm00051" Warning message: Don't understand the SOAP type `string' yet in: fromSOAP(x, type = type, root = root, converters = converters, > get.pathways.by.genes(query_vector[1:3]) NULL To summarise: 1) get.pathways.by.genes returns warning messages 2) get.pathways.by.genes returns an incorrect result when given a vector of genes of length 1 3) get.pathways.by.genes returns inconsistent results when given vectors of different sizes, one of which contains genes that do not exist in a KEGG pathway I've had similar issues with the perl access to KEGG and raised this with the helpdesk years ago. Does anyone else have these issues? Thanks Mick