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https://stat.ethz.ch/mailman/listinfo/bioconductor Martin Aaron Wolen <wole...@vcu.edu> writes: > I'm trying to identify the positions of all genes within a specific > chromosomal region using biomart. When using the current biomart > database I'm able to do this without issue. However, I need to use > build 36 of the mouse genome which was last included in ensembl mart > 46. I selected this mart and the mouse dataset as follows: > > mart<-useMart(biomart="ensembl_mart_46", host="www.biomart.org", > path="/biomart/martservice", port=80, archive=TRUE) > > mart<-useDataset("mmusculus_gene_ensembl", mart=mart) > > I'm able to list the available attributes and filters just fine, but > when I attempt to actually retrieve data using getBM() I receive the > following error: > > > genes<-getBM(attributes=c("ensembl_gene_id", "external_gene_id", > "description", "chromosome_name", "start_position", > "transcript_start"), > + filters=c("chromosome_name","start","end"), > + values=list(12,40000000,70000000), > + mart=mart) > Error in listFilters(mart, what = "type") : > The function argument 'what' contains an invalid value: type > Valid are: name, description, options, fullDescription > > The same error is returned if I check to see what value type is > required for a particular filter: > > > filterType("chromosome_name", mart=mart) > Error in listFilters(mart, what = "type") : > The function argument 'what' contains an invalid value: type > Valid are: name, description, options, fullDescription > > I'd really appreciate some help with this issue. > > Cheers, > Aaron > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.