Question: Re: KEGGprofile: "Error in phyper - Non-numeric argument to mathematical function" when using non model organism
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gravatar for zhao shilin
4.5 years ago by
zhao shilin60
zhao shilin60 wrote:
Dear Stefano, I've tested species Pseudovibrio FO-BEG1 ("psf" in KEGG database) and found it was imported into KEGG database in 2013 ( http://www.genome.jp/kegg-bin/show_organism?org=psf). But KEGG.db package was updated until 2012. I think that is the reason for the error message. Now I provide a new parameter "download_latest" in "find_enriched_pathway" function of KEGGprofile package, you can find it in KEGGprofile version 1.7.6 on Bioconductor. But I think it is still in the develop channel of Bioconductor so you may not able to see it immediately. You can download it from my github (https://github.com/slzhao/KEGGprofile) now. Here is the test codes: library("KEGGprofile") species<-"psf" download_KEGGfile(pathway_id="00010",species=species) result<-parse_XMLfile(pathway_id="00010",species=species) genes<-unique(result[9:40,1]) genes enriched<-find_enriched_pathway(gene=genes,species=species, download_latest=TRUE) enriched$stastic Please let me know if you have any other questions. Best, Shilin 2014-09-14 2:07 GMT-05:00 stefano romano <stfn.romano@gmail.com>: > Dear Shilin, > thank you very much for your answer. > The organism I am using is Pseudovibrio FO-BEG1. > > I got the same problme with both GI and locus_tag. > > > These are some GI: > 359341142 > 359341144 > 359341148 > 359341161 > 359341162 > 359341167 > 359341173 > 359341177 > 359341200 > 359341208 > 359341211 > > And these are some locus-tag: > > PSE_3630PSE_4282PSEp_0373PSE_1587PSE_1679PSE_1691PSE_1086PSE_0648PSE _1681 > PSE_2573 > > Thanks again for your help. > > Best, > > Stefano > > 2014-09-14 3:36 GMT+02:00 zhao shilin <zhaoshilin@gmail.com>: > >> Dear Stafano, >> >> I think the ID from the non model organism may cause the error. Would >> you please tell me the specie you tested and send me some of your genes. >> So that I can have a try. >> Thank you! >> >> Best, >> Shilin >> >> 2014-09-13 3:03 GMT-05:00 stefano romano <stfn.romano@gmail.com>: >> >>> Hi, >>> >>> I am using KEGGprofile to perform KEGG enrichment for a non model >>> organism. >>> Using the data from the R documentation i perfectely obtaine the >>> enrichment. >>> >>> >data(pho_sites_count) >>> >genes<-names(rev(sort(pho_sites_count[,1]))[1:300]) >>> > summary(genes) >>> Length Class Mode >>> 300 character character >>> > is.vector(genes) >>> [1] TRUE >>> >pho_KEGGresult<-find_enriched_pathway(genes,specis='hsa') >>> >>> However, when I use my datasets, which I submit as character vector with >>> NCBI ID, I get the following error: >>> >>> Error in phyper(kegg_result_length[x], keggpathway2gene_length[x], >>> length(unique(unlist(keggpathway2gene))) - : >>> Non-numeric argument to mathematical function >>> >>> Any suggestion how to overcome this problem? >>> >>> Thank you very much. >>> >>> [[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]] _______________________________________________ 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
organism keggprofile • 807 views
ADD COMMENTlink written 4.5 years ago by zhao shilin60
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