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Question: Kegg Profile package problem
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gravatar for gregory voisin
6.0 years ago by
Canada
gregory voisin430 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') #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 était '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 Montréal Dim, 16 déc. 2012 à 11:10 16 déc Mail affecté d’une étoile de gregory voisin à 1 destinataire Problem to download Kegg map from KEGGprofile package Afficher les détails * * 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') #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 était '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 Montréal > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=French_Canada.1252  LC_CTYPE=French_Canada.1252   [3] LC_MONETARY=French_Canada.1252 LC_NUMERIC=C                 [5] LC_TIME=French_Canada.1252    attached base packages: [1] stats     graphics  grDevices utils     datasets  methods  base     other attached packages:  [1] KEGGprofile_1.0.0    KEGG.db_2.8.0        RSQLite_0.11.2      [4] DBI_0.2-5            AnnotationDbi_1.20.0 Biobase_2.18.0      [7] BiocGenerics_0.4.0   TeachingDemos_2.8    png_0.1-4          [10] XML_3.95-0.1        loaded via a namespace (and not attached): [1] IRanges_1.16.2  parallel_2.15.0 stats4_2.15.0 [[alternative HTML version deleted]]
ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by gregory voisin430
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gravatar for gregory voisin
6.0 years ago by
Canada
gregory voisin430 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') #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 était '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 Montréal [[alternative HTML version deleted]]
ADD COMMENTlink written 6.0 years ago by gregory voisin430
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
ADD REPLYlink written 6.0 years ago by Dan Tenenbaum ♦♦ 8.2k
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(). Greg ________________________________ De : Dan Tenenbaum <dtenenba@fhcrc.org> Cc : "bioconductor@r-project.org" <bioconductor@r-project.org> Envoyé le : Jeudi 27 décembre 2012 2h35 Objet : Re: [BioC] Kegg Profile package problem > > > > 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 était '404 Not Found' > > > My solution :  omit this pathway in my analysis: ponctual, fast  but [[elided Yahoo spam]] > > If someone has a suggestion , comments or solution, let's go , > > Thanks > > Greg > Montréal > >        [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD REPLYlink written 6.0 years ago by gregory voisin430
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 > >
ADD REPLYlink written 6.0 years ago by Dan Tenenbaum ♦♦ 8.2k
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". Greg ________________________________ De : Dan Tenenbaum <dtenenba@fhcrc.org> Cc : "bioconductor@r-project.org" <bioconductor@r-project.org> Envoyé le : Jeudi 27 décembre 2012 14h39 Objet : Re: [BioC] Kegg Profile package problem > 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@fhcrc.org> > Cc : "bioconductor@r-project.org" <bioconductor@r-project.org> > Envoyé le : Jeudi 27 décembre 2012 2h35 > Objet : Re: [BioC] Kegg Profile package problem > te: >> >> >> >> 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 était '404 Not Found' >> >> >> My solution :  omit this pathway in my analysis: ponctual, fast but not [[elided Yahoo spam]] >> >> If someone has a suggestion , comments or solution, let's go , >> >> Thanks >> >> Greg >> Montréal >> >>        [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]
ADD REPLYlink written 6.0 years ago by gregory voisin430
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 >> >> > >
ADD REPLYlink written 6.0 years ago by Dan Tenenbaum ♦♦ 8.2k
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 >>> >>> >> >>
ADD REPLYlink written 6.0 years ago by zhao shilin60
Hi Shilin, Thanks for your answers Greg ________________________________ De : zhao shilin <zhaoshilin@gmail.com> À : Dan Tenenbaum <dtenenba@fhcrc.org> bioconductor@r-project.org> Envoyé le : Vendredi 28 décembre 2012 2h05 Objet : Re: [BioC] Kegg Profile package problem 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@fhcrc.org>: ote: >> >> 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@fhcrc.org> >> Cc : "bioconductor@r-project.org" <bioconductor@r-project.org> >> Envoyé le : Jeudi 27 décembre 2012 14h39 >> >> Objet : Re: [BioC] Kegg Profile package problem >> ote: >>> 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@fhcrc.org> >>> Cc : "bioconductor@r-project.org" <bioconductor@r-project.org> >>> Envoyé le : Jeudi 27 décembre 2012 2h35 >>> Objet : Re: [BioC] Kegg Profile package problem >>> >>> 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 était '404 Not Found' >>>> >>>> >>>> My solution :  omit this pathway in my analysis: ponctual, fast but not [[elided Yahoo spam]] >>>> >>>> If someone has a suggestion , comments or solution, let's go , >>>> >>>> Thanks >>>> >>>> Greg >>>> Montréal >>>> >>>>        [[alternative HTML version deleted]] >>>> >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> >> [[alternative HTML version deleted]]
ADD REPLYlink written 6.0 years ago by gregory voisin430
For your information, 3 weeks ago, I subscribed to Amazon web services to use R studio and bioconductor. Here, I highlight a problem about the weird bill associated to the Amazon web services: When you create a stack , a stockage volume is created and normally when you delete a stack,the stockage volume is deleted too. But, in my case, the deletion of volume was problematic and after, 3 weeks of usage, I had 40 stockage volume ( 40 gig by volume)associated to my Amazon account and I have paid for that ( the first 40 gig is free). The charge for that is not important ( 20 $CA for 3 weeks) but could be more important if you don't check. It's not very clear if it's a lack of understanding of me or if it's a technical problem associated to web service when you delete your instance, check your stockage volume: 1.http://aws.amazon.com/fr/console/ 2. connect to AWS console 3. click on EC2 ( virtual servers in the cloud) 4. In part " My services" : check EBS volume(normally :0) Greg  Montreal ________________________________ De : Dan Tenenbaum <dtenenba@fhcrc.org> Cc : "bioconductor@r-project.org" <bioconductor@r-project.org> Envoyé le : Jeudi 27 décembre 2012 2h35 Objet : Re: [BioC] Kegg Profile package problem > > > > 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 était '404 Not Found' > > > My solution :  omit this pathway in my analysis: ponctual, fast  but [[elided Yahoo spam]] > > If someone has a suggestion , comments or solution, let's go , > > Thanks > > Greg > Montréal > >        [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD REPLYlink written 6.0 years ago by gregory voisin430
Hi Greg, On Thu, Dec 27, 2012 at 7:04 AM, gregory voisin <voisingreg at="" yahoo.fr=""> wrote: > For your information, > 3 weeks ago, I subscribed to Amazon web services to use R studio and > bioconductor. > Here, I highlight a problem about the weird bill associated to the Amazon > web services: > > When you create a stack , a stockage volume is created and normally when you > delete a stack,the stockage volume is deleted too. > > But, in my case, the deletion of volume was problematic and after, 3 weeks > of usage, I had 40 stockage volume ( 40 gig by volume)associated to my > Amazon account and I have paid for that ( the first 40 gig is free). The > charge for that is not important ( 20 $CA for 3 weeks) but could be more > important if you don't check. > > It's not very clear if it's a lack of understanding of me or if it's a > technical problem associated to web service > > when you delete your instance, check your stockage volume: > 1.http://aws.amazon.com/fr/console/ > 2. connect to AWS console > 3. click on EC2 ( virtual servers in the cloud) > 4. In part " My services" : check EBS volume(normally :0) > I've changed our public AMIs so that EBS volumes that are created when instances are launched, are now deleted when the instances are terminated. So this problem will no longer occur. Thanks, Dan > Greg > Montreal > > > > > > ________________________________ > 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 > >
ADD REPLYlink written 6.0 years ago by Dan Tenenbaum ♦♦ 8.2k
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