Hi Amanda, This is now also fixed in the release branch. http://bioconductor.org/packages/2.2/bioc/html/GenomeGraphs.html or update with biocLite script. Cheers, Steffen > Amanda. > > Have a look at Steffen's recent post: > https://stat.ethz.ch/pipermail/bioconductor/2008-August/023714.html > > Basically, some internal changes to attribute names at biomart/ > ensembl. I think you have two options: > > 1. Install the BioC 2.3 version of GenomeGraphs. > 2. Use 'listAttributes' (as the error message states) to get the > updated attribute names. > > Cheers, > Mark > > On 05/08/2008, at 1:04 PM, Amanda Miotto wrote: > >> >> In regards to the library GenomeGraphs, when I try to define a Gene, >> I get >> the following error. I am following the instructions from The >> GenomeGraphs >> user???s guide by Steffen Durinck???and James Bullard???. Where would >> I be going >> wrong? Also, I am curious about the structure of gene, as I am >> trying to >> replicate it with RMySQL, having set up a mysql identical to the >> ensembl >> one. In the list listAttributes, ensembl_gene_id is in there. >> Thanks, >> >> >>> gene = new("Gene", id = "ENSG00000095203",type = "ensembl_gene_id", >> biomart = mart) >> Error in getBM(c("structure_gene_stable_id", >> "structure_transcript_stable_id", : >> Invalid attribute(s): structure_exon_stable_id, >> structure_exon_chrom_start, structure_exon_chrom_end, >> structure_exon_rank >> Please use the function 'listAttributes' to get valid attribute names >> >> Amanda Miotto >> a.miotto at griffith.edu.au >> >> Software Engineer. >> Research Computing Services >> INFORMATION SERVICES >> Griffith University, NATHAN 4111, AUSTRALIA >> Phone: +61 7 37354419 Fax: +61 7 37356650 >> Web: http://eResearch.griffith.edu.au/ >> >> PRIVILEGED - PRIVATE AND CONFIDENTIAL: >> This email and any files transmitted with it are intended solely for >> the use of the addressee(s) and may contain information which is >> confidential or privileged. If you receive this email and you are >> not the addressee(s) [or responsible for delivery of the email to the >> addressee(s)], please disregard the contents of the email, delete the >> email and notify the author immediately. >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > ------------------------------ > Mark Robinson > Epigenetics Laboratory, Garvan > Bioinformatics Division, WEHI > e: m.robinson at garvan.org.au > e: mrobinson at wehi.edu.au > p: +61 (0)3 9345 2628 > f: +61 (0)3 9347 0852 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor