Hi Dan, I'm very happy to know that some other persons were using my package. And it is the first time that some persons ask me questions about it in the mail list. For your question, the web page "http://www.genome.jp/kegg/pathway/map/map00910.html" indicated that: The biological process of the nitrogen cycle is a complex interplay among many microorganisms catalyzing different reactions. And we can't find human in the reference pathway tab of this page. So I think this is not a human pathway. And what you said about the download_KEGGfile function is right. Because I want to download the species specific pathway map with green background to indicate that the gene exist in this species. Maybe I will change function as your advise in the next version. For the find_enriched_pathway function, it used the annotation from the package KEGG.db. I have tested the KEGG.db package and some genes were annotated to hsa00910 pathway. I don't know why this happens. Maybe it is because of the update of the KEGG website. Shilin 2012/12/28 Dan Tenenbaum <dtenenba at="" fhcrc.org="">: > On Thu, Dec 27, 2012 at 12:58 PM, gregory voisin <voisingreg at="" yahoo.fr=""> wrote: >> >> In that case, can you get the pathway map you need from this link: >> http://www.genome.jp/kegg/pathway/map/map00910.png ? >> >> In the automatic workflux ( my case), it isn't very optimal >> >> I imagie that download_KEGGfile function concatenate >> (pathway_id="00910",specis='hsa') to build the request: >> 'http://www.genome.jp/kegg-bin/download?entry=hsa00910&format=kgml' >> >> Ideally the hsa could be replaced by "map". >> > > I'm cc'ing the maintainer of the KEGGprofile package. > > Dan > > >> Greg >> >> >> >> ________________________________ >> De : Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> ? : gregory voisin <voisingreg at="" yahoo.fr=""> >> Cc : "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> >> Envoy? le : Jeudi 27 d?cembre 2012 14h39 >> >> Objet : Re: [BioC] Kegg Profile package problem >> >> On Thu, Dec 27, 2012 at 4:30 AM, gregory voisin <voisingreg at="" yahoo.fr=""> wrote: >>> Hi Dan , >>> Yes, the link associated to hsa00910 doesn't exist but the map00910 >>> (http://www.genome.jp/kegg/pathway/map/map00910.html) exists >>> >>> The id 00910 is a result provided by the find_enriched_pathway function(). >>> >> >> In that case, can you get the pathway map you need from this link: >> >> http://www.genome.jp/kegg/pathway/map/map00910.png >> >> >> ? >> >> Dan >> >>> Greg >>> >>> >>> >>> ________________________________ >>> De : Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >>> ? : gregory voisin <voisingreg at="" yahoo.fr=""> >>> Cc : "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> >>> Envoy? le : Jeudi 27 d?cembre 2012 2h35 >>> Objet : Re: [BioC] Kegg Profile package problem >>> >>> On Wed, Dec 26, 2012 at 6:54 AM, gregory voisin <voisingreg at="" yahoo.fr=""> >>> wrote: >>>> >>>> >>>> >>>> Hi, >>>> I use KeggProfile in my pipeline analysis and it's efficient, but I have >>>> problem with one pathway_ID. >>>> >>>> Exemple ( copy and paste): >>>> >>>> require(KEGGprofile) >>>> download_KEGGfile(pathway_id="04110",specis='hsa') >>>> >>>> #In this case , not problem >>>> >>>> download_KEGGfile(pathway_id="00910",specis='hsa') >>> >>> >>> I think perhaps there is no such pathway. Here's a list of all human >>> pathways: >>> http://rest.kegg.jp/list/pathway/hsa >>> >>> 04110 is included but 00910 is not. >>> >>> Dan >>> >>> >>>> >>>> #this pahway exits in KEGG, but the download is impossible >>>> #[1] "Downloading files: 1/1" >>>> #essai de l'URL >>>> 'http://www.genome.jp/kegg- bin/download?entry=hsa00910&format=kgml' >>>> #Content type 'text/plain' length unknown >>>> #URL ouverte >>>> #downloaded 1 bytes >>>> >>>> #essai de l'URL 'http://www.genome.jp/kegg/pathway/hsa/hsa00910.png' >>>> #Erreur dans download.file(paste("http://www.genome.jp/kegg/pathway/", >>>> specis, : >>>> # impossible d'ouvrir l'URL >>>> 'http://www.genome.jp/kegg/pathway/hsa/hsa00910.png' >>>> #De plus : Message d'avis : >>>> #In download.file(paste("http://www.genome.jp/kegg/pathway/", specis, : >>>> # ouverture impossible : le statut HTTP ?tait '404 Not Found' >>>> >>>> >>>> My solution : omit this pathway in my analysis: ponctual, fast but not >>>> very elegant and not professional !! >>>> >>>> If someone has a suggestion , comments or solution, let's go , >>>> >>>> Thanks >>>> >>>> Greg >>>> Montr?al >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >> >>