KEGGprofile: "Error in phyper - Non-numeric argument to mathematical function" when using non model organism
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artur ▴ 80
@artur-6730
Last seen 5.2 years ago
Germany
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]]
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zhao shilin ▴ 60
@zhao-shilin-5674
Last seen 6.6 years ago
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 at="" 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 at 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]]
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