Hello, I am rerunning code I had using biomaRt. But I believe there is a change in the attributes. Before, everything was 'structure_xyz' from the Structure category: anno <- getBM(c("structure_gene_stable_id", "structure_transcript_stable_id", "structure_exon_stable_id", "structure_chrom_name", "structure_transcript_chrom_strand", "structure_exon_chrom_start", "structure_exon_chrom_end", "structure_exon_rank", "structure_biotype"), mart = mart) Now it appears that it's just structure_transcript_stable_id, but the other attributes are under Gene or Exon, rather than Structure. I don't really know the distinction in this. Is it okay to mix these terms like I do here: annoNew <- getBM(c("ensembl_gene_id", "structure_transcript_stable_id", "ensembl_exon_id", "exon_chrom_start", "exon_chrom_end", "strand", "chromosome_name", "biotype"), mart = mart) I've run the code and don't see any obvious problems, but I would like to be sure -- it's hard to find out if there's a problem on just a tiny number of genes. Thanks for any help, Elizabeth UC, Berkeley

Thanks Amanda for your response. I guess I was not clear in my post. I did put the new attributes from listAttributes() in my code (I listed both my old code and my new code so it was clear what I had done and now what I was trying to do). I'm just not sure if I'm using the new attribute names correctly. Previously I had to use special 'Structure' attributes to get the gene id, chromosome, etc. pulled down along with the transcript and exon information (or at least I thought I did). Now those attributes no longer exist. My new code assumes that now it just has a single identifier and there's no problem using the same 'ensembl_gene_id' attribute regardless of the category of other attributes are being pulled down with it. But I would like to know that this is correct because I am not comfortable with what these things mean and I don't want to have a hidden error somewhere. Thanks a lot, Elizabeth Amanda Miotto wrote: > They upgraded. Have a look at the following posts:- > > > >> 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 >> > > > > > 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. >