Question: A bug in either KEGG or KEGGSOAP?
0
gravatar for Sang Chul Choi
7.8 years ago by
Sang Chul Choi230 wrote:
Hi, I am wondering if this is an old bug eighter in KEGG or KEGGSOAP (v1.28.0). The version of R is R version 2.14.1 (2011-12-22). I installed KEGGSOAP, and tried to list pathways. While list.pathways lists 44, the KEGG website shows 88 pathways. http://www.genome.jp/dbget-bin/get_linkdb?-t+pathway+gn:T00100 http://www.genome.jp/dbget-bin/www_bget?gn:T00100 Thank you, SangChul > source("http://www.bioconductor.org/biocLite.R") > biocLite("KEGGSOAP") > library(KEGGSOAP) > y <- list.pathways("smu") > length(y) [1] 44 > sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] KEGGSOAP_1.28.0 BiocInstaller_1.2.1 goseq_1.6.0 [4] BiasedUrn_1.04 geneLenDataBase_0.99.8 RColorBrewer_1.0-5 [7] maptools_0.8-14 sp_0.9-93 foreign_0.8-48 [10] xtable_1.6-0 DESeq_1.6.1 locfit_1.5-6 [13] lattice_0.20-0 akima_0.5-7 Biobase_2.14.0 [16] plotrix_3.3-3 GenomicRanges_1.6.4 IRanges_1.12.5
pathways keggsoap • 629 views
ADD COMMENTlink modified 7.8 years ago by Marc Carlson7.2k • written 7.8 years ago by Sang Chul Choi230
Answer: A bug in either KEGG or KEGGSOAP?
0
gravatar for Marc Carlson
7.8 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi SangChui, The discrepancy you are seeing is hard to explain from the bioconductor code for this function. The KEGGSOAP package is basically parsing data from a service on the KEGG site. The only code in the actual KEGGSOAP package is what is needed to talk to the SOAP services provided by KEGG. So the fact that the function is working and producing an output means that it is unlikely that there is a bug in KEGGSOAP. There is nothing in the KEGGSOAP package that tries to limit the number or pathways returned. So it seems that the most likely cause for this kind of discrepancy is that the SOAP service and the KEGG website are somehow out of sync with each other. Marc ----- Original Message ----- From: "Sang Chul Choi" <schoi@cornell.edu> To: bioconductor at r-project.org Sent: Monday, January 23, 2012 11:59:21 AM Subject: [BioC] A bug in either KEGG or KEGGSOAP? Hi, I am wondering if this is an old bug eighter in KEGG or KEGGSOAP (v1.28.0). The version of R is R version 2.14.1 (2011-12-22). I installed KEGGSOAP, and tried to list pathways. While list.pathways lists 44, the KEGG website shows 88 pathways. http://www.genome.jp/dbget-bin/get_linkdb?-t+pathway+gn:T00100 http://www.genome.jp/dbget-bin/www_bget?gn:T00100 Thank you, SangChul > source("http://www.bioconductor.org/biocLite.R") > biocLite("KEGGSOAP") > library(KEGGSOAP) > y <- list.pathways("smu") > length(y) [1] 44 > sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] KEGGSOAP_1.28.0 BiocInstaller_1.2.1 goseq_1.6.0 [4] BiasedUrn_1.04 geneLenDataBase_0.99.8 RColorBrewer_1.0-5 [7] maptools_0.8-14 sp_0.9-93 foreign_0.8-48 [10] xtable_1.6-0 DESeq_1.6.1 locfit_1.5-6 [13] lattice_0.20-0 akima_0.5-7 Biobase_2.14.0 [16] plotrix_3.3-3 GenomicRanges_1.6.4 IRanges_1.12.5 _______________________________________________ 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 COMMENTlink written 7.8 years ago by Marc Carlson7.2k
Hi SangChul You may get some insight into what the problem is if you contact the KEGG stuff at: http://www.genome.jp/feedback/ then specify "KEGG API" in the options. Since there has been a lot of structural changes in KEGG recently it may be a transient problem. Diego On Tue, Jan 24, 2012 at 6:24 PM, Carlson, Marc R <mcarlson at="" fhcrc.org=""> wrote: > Hi SangChui, > > The discrepancy you are seeing is hard to explain from the bioconductor code for this function. ?The KEGGSOAP package is basically parsing data from a service on the KEGG site. ?The only code in the actual KEGGSOAP package is what is needed to talk to the SOAP services provided by KEGG. ?So the fact that the function is working and producing an output means that it is unlikely that there is a bug in KEGGSOAP. ?There is nothing in the KEGGSOAP package that tries to limit the number or pathways returned. ?So it seems that the most likely cause for this kind of discrepancy is that the SOAP service and the KEGG website are somehow out of sync with each other. > > > ?Marc > > > ----- Original Message ----- > From: "Sang Chul Choi" <schoi at="" cornell.edu=""> > To: bioconductor at r-project.org > Sent: Monday, January 23, 2012 11:59:21 AM > Subject: [BioC] A bug in either KEGG or KEGGSOAP? > > Hi, > > I am wondering if this is an old bug eighter in KEGG or KEGGSOAP (v1.28.0). ?The version of R is R version 2.14.1 (2011-12-22). > > I installed KEGGSOAP, and tried to list pathways. ?While list.pathways lists 44, the KEGG website shows 88 pathways. > > http://www.genome.jp/dbget-bin/get_linkdb?-t+pathway+gn:T00100 > http://www.genome.jp/dbget-bin/www_bget?gn:T00100 > > Thank you, > > SangChul > >> source("http://www.bioconductor.org/biocLite.R") >> biocLite("KEGGSOAP") >> library(KEGGSOAP) >> y <- list.pathways("smu") >> length(y) > [1] 44 > >> sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > ?[1] KEGGSOAP_1.28.0 ? ? ? ?BiocInstaller_1.2.1 ? ?goseq_1.6.0 > ?[4] BiasedUrn_1.04 ? ? ? ? geneLenDataBase_0.99.8 RColorBrewer_1.0-5 > ?[7] maptools_0.8-14 ? ? ? ?sp_0.9-93 ? ? ? ? ? ? ?foreign_0.8-48 > [10] xtable_1.6-0 ? ? ? ? ? DESeq_1.6.1 ? ? ? ? ? ?locfit_1.5-6 > [13] lattice_0.20-0 ? ? ? ? akima_0.5-7 ? ? ? ? ? ?Biobase_2.14.0 > [16] plotrix_3.3-3 ? ? ? ? ?GenomicRanges_1.6.4 ? ?IRanges_1.12.5 > _______________________________________________ > 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 > > _______________________________________________ > 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 7.7 years ago by Diego Diez730
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