I keep running into the same error when trying to do a genes-to- pathways request in the KEGGsoap package: I'm new to the package, but as I understand it I should be able to pass a vector of gene IDs and receive back a vector of pathway IDs, however I keep getting a 'xmlns: URI SOAP/KEGG is not absolute' error. This appears to be something to do with the URL for the SOAP server: >> genes > [1] "hsa:728819" "hsa:100129239" "hsa:441150" "hsa:440905" "hsa:389493" "hsa:645954" > [7] "hsa:283711" "hsa:400645" "hsa:100128416" "hsa:100128542" >> get.pathways.by.genes(genes) > xmlns: URI SOAP/KEGG is not absolute > xmlns: URI SOAP/KEGG is not absolute > character(0) >> >> KEGGserver <- SOAPServer("http://soap.genome.jp/keggapi/request_v6.0.cgi") >> .SOAP(KEGGserver, "get_pathways_by_genes", > + .soapArgs=list('genes_id_list' = genes), > + action = KEGGaction, nameSpaces = SOAPNameSpaces(version=1)) > xmlns: URI SOAP/KEGG is not absolute > xmlns: URI SOAP/KEGG is not absolute > character(0) >> >> There does seem to have been a similar error in relation to the biomaRt package, but I can't see an obvious fix to apply here and I don't seem to be able to find where within the SOAP method this is coming from; if anyone's encountered this before and/or has any advice to offer I'd much appreciate it. thanks -s

Hi seth -- On 01/07/2012 09:58 AM, seth redmond wrote: > I keep running into the same error when trying to do a genes-to- pathways request in the KEGGsoap package: > > I'm new to the package, but as I understand it I should be able to pass a vector of gene IDs and receive back a vector of pathway IDs, however I keep getting a 'xmlns: URI SOAP/KEGG is not absolute' error. This appears to be something to do with the URL for the SOAP server: > >>> genes >> [1] "hsa:728819" "hsa:100129239" "hsa:441150" "hsa:440905" "hsa:389493" "hsa:645954" >> [7] "hsa:283711" "hsa:400645" "hsa:100128416" "hsa:100128542" >>> get.pathways.by.genes(genes) >> xmlns: URI SOAP/KEGG is not absolute >> xmlns: URI SOAP/KEGG is not absolute >> character(0) I think the xmlns: message is not the problem. Instead, I think (a) some of your id's do not map to any pathway and (b) get.genes.by.pathway is doing an intersection of pathways for each gene. For instance... > paths <- list.pathways("hsa") > (geneids <- get.genes.by.pathway(paths[[1]]@entry_id)) [1] "hsa:1431" "hsa:1737" "hsa:1738" "hsa:1743" "hsa:2271" "hsa:3417" [7] "hsa:3418" "hsa:3419" "hsa:3420" "hsa:3421" "hsa:4190" "hsa:4191" [13] "hsa:47" "hsa:48" "hsa:4967" "hsa:50" "hsa:5091" "hsa:5105" [19] "hsa:5106" "hsa:5160" "hsa:5161" "hsa:5162" "hsa:55753" "hsa:6389" [25] "hsa:6390" "hsa:6391" "hsa:6392" "hsa:8801" "hsa:8802" "hsa:8803" > get.pathways.by.genes(geneids[1]) [1] "path:hsa00020" "path:hsa00630" "path:hsa01100" > get.pathways.by.genes(geneids[2]) [1] "path:hsa00010" "path:hsa00020" "path:hsa00620" "path:hsa01100" > get.pathways.by.genes(geneids[1:2]) [1] "path:hsa00020" "path:hsa01100" Martin >>> >>> KEGGserver<- SOAPServer("http://soap.genome.jp/keggapi/request_v6.0.cgi") >>> .SOAP(KEGGserver, "get_pathways_by_genes", >> + .soapArgs=list('genes_id_list' = genes), >> + action = KEGGaction, nameSpaces = SOAPNameSpaces(version=1)) >> xmlns: URI SOAP/KEGG is not absolute >> xmlns: URI SOAP/KEGG is not absolute >> character(0) >>> >>> > > There does seem to have been a similar error in relation to the biomaRt package, but I can't see an obvious fix to apply here and I don't seem to be able to find where within the SOAP method this is coming from; if anyone's encountered this before and/or has any advice to offer I'd much appreciate it. > > thanks > > -s > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793