Hi, I need to re-run a 6 month-old chunk of code but I get an error with biomaRt when calling the uniprot_mart.: " Incorrect BioMart name, use the listMarts function to see which BioMart databases are available" A mart named unimart seems to replace it (?) but no dataset is attached to it. Is the uniprot_mart deprecated or defunct, or it's a bug? What mart should I use to annotate Uniprot ID (protein name and functional annotation) ? Thanks Nolwenn Le Meur sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] grid stats graphics grDevices utils [6] datasets methods base other attached packages: [1] biomaRt_2.6.0 xtable_1.5-6 [3] ppiStats_1.16.0 ppiData_0.1.14 [5] lattice_0.19-17 ScISI_1.22.0 [7] apComplex_2.16.0 GO.db_2.4.5 [9] RSQLite_0.9-4 DBI_0.2-5 [11] RpsiXML_1.10.0 hypergraph_1.22.0 [13] XML_3.2-0 annotate_1.28.0 [15] AnnotationDbi_1.12.0 Biobase_2.10.0 [17] RBGL_1.26.0 Rgraphviz_1.28.0 [19] graph_1.28.0 loaded via a namespace (and not attached): [1] Category_2.16.0 GSEABase_1.12.2 [3] RColorBrewer_1.0-2 RCurl_1.4-3 [5] genefilter_1.32.0 org.Sc.sgd.db_2.4.6 [7] splines_2.12.1 survival_2.36-2 [9] tools_2.12.1

Hi Nolwenn, On 2/11/2011 10:19 AM, Le Meur-Rouillard, Nolwenn wrote: > Hi, > > I need to re-run a 6 month-old chunk of code but I get an error with > biomaRt when calling the uniprot_mart.: > > " Incorrect BioMart name, use the listMarts function to see which > BioMart databases are available" > > A mart named unimart seems to replace it (?) but no dataset is > attached to it. Is the uniprot_mart deprecated or defunct, or it's a > bug? What mart should I use to annotate Uniprot ID (protein name and > functional annotation) ? Not familiar with the uniprot_mart, and you don't mention species. However, if your species isn't too exotic, can't you just use ensembl? For instance, the hsapiens_gene_ensembl lists these: 79 uniprot_sptrembl UniProt/TrEMBL Accession 80 uniprot_swissprot UniProt/SwissProt ID 81 uniprot_swissprot_accession UniProt/SwissProt Accession Best, Jim > > Thanks Nolwenn Le Meur > > > > sessionInfo() R version 2.12.1 (2010-12-16) Platform: > x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: [1] C > > attached base packages: [1] grid stats graphics grDevices > utils [6] datasets methods base > > other attached packages: [1] biomaRt_2.6.0 xtable_1.5-6 [3] > ppiStats_1.16.0 ppiData_0.1.14 [5] lattice_0.19-17 > ScISI_1.22.0 [7] apComplex_2.16.0 GO.db_2.4.5 [9] RSQLite_0.9-4 > DBI_0.2-5 [11] RpsiXML_1.10.0 hypergraph_1.22.0 [13] XML_3.2-0 > annotate_1.28.0 [15] AnnotationDbi_1.12.0 Biobase_2.10.0 [17] > RBGL_1.26.0 Rgraphviz_1.28.0 [19] graph_1.28.0 > > loaded via a namespace (and not attached): [1] Category_2.16.0 > GSEABase_1.12.2 [3] RColorBrewer_1.0-2 RCurl_1.4-3 [5] > genefilter_1.32.0 org.Sc.sgd.db_2.4.6 [7] splines_2.12.1 > survival_2.36-2 [9] tools_2.12.1 > > _______________________________________________ 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues