Question: Error in example from biomaRt vignette
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gravatar for Steffen Durinck
6.0 years ago by
Steffen Durinck90 wrote:
Hi Tommaso, This is a recently discovered error and the BioMart people are looking into it. I've CC'd the bioconductor email list to let others know about the solution below. You need to query the ensembl BioMart directly at Ensembl as follows: ensembl = useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl",host=" www.ensembl.org") protein = getBM(c("entrezgene","peptide"),filters="entrezgene",values=c(100, 5728), mart=ensembl) > protein entrezgene 1 100 2 100 3 100 4 5728 5 5728 6 100 7 100 peptide 1 MAQTPAFDKPKVELHVHLDGSIKPETILYYGRRRGIALPANTAEGLLNVIGMDKPLTLPDFLAKFDYYMP AIAGCREAIKRIAYEFVEMKAKEGVVYVEVRYSPHLLANSKVEPIPWNQAEGDLTPDEVVALVGQGLQEG ERDFGVKARSILCCMRHQPNWSPKVVELCKKYQQQTVVAIDLAGDETIPGSSLLPGHVQAYQEAVKSGIH RTVHAGEVGSAEVVKEAVDILKTERLGHGYHTLEDQALYNRLRQENMHFEAQK* 2 MAQTPAFDKPKVELHVHLDGSIKPETILYYGRRRGIALPANTAEGLLNVIGMDKPLTLPDFLAKFDYYMP AIARL* 3 Cheers, Steffen On Thu, May 9, 2013 at 6:28 AM, Tommaso Leonardi <tl344@ebi.ac.uk> wrote: > Dear Steffen, > My name is Tom and I'm a student in the Enright group at EBI. I've > just come across this error while going through one of the examples in > the biomaRt vignette: > > > library("biomaRt") > > ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") > > protein = getSequence(id=c(100, > 5728),type="entrezgene",seqType="peptide", mart=ensembl) > Error in getBM(c(seqType, type), filters = type, values = id, mart = mart, > : > Query ERROR: caught BioMart::Exception::Database: Error during query > execution: Can't create/write to file > '/mnt/ephemeral0/mysqltmp/#sql_40a_0.MYI' (Errcode: 2) > > I'm not sure if this is due to a mistake I make or if it's a bug. Any > info is very appreciated :) > The sessionInfo is reported below. > > Thank you very much in advance and best regards > tom > > > > > sessionInfo() > R version 3.0.0 (2013-04-03) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.16.0 BiocInstaller_1.10.1 > > loaded via a namespace (and not attached): > [1] RCurl_1.95-4.1 tools_3.0.0 XML_3.95-0.2 > > > > -- > Tommaso Leonardi - PhD student > Enright group (EMBL-EBI) and > Pluchino group (John van Geest Centre for Brain Repair) > EMBL-EBI, Wellcome Trust Genome Campus > Hinxton, CB10 1SD > UK > [[alternative HTML version deleted]]
biomart brain • 503 views
ADD COMMENTlink written 6.0 years ago by Steffen Durinck90
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