Hi Marco, There is a better attribute to query the start and end positions of genes, use the following query: gene.list <- getBM(c("entrezgene","chr_name","chrom_start","chrom_end"), filters="chr_name",values=1, mart=ensmart) Best regards, Steffen -----Original Message----- From: marco zucchelli [mailto:marco.bioc@gmail.com] Sent: Mon 7/2/2007 5:25 AM To: bioconductor; Durinck, Steffen (NIH/NCI) [F] Subject: [BioC] Biomart with human genes NCBI 35 Dear Steffen, thanks for your help! Works fine but seems like there are other problems with the archived versions. I would like to get the positions of the genes on chromosome 1 but seems like I cannot do that running mysql (see below) Do you have any idea about how to bypass the problem ? ########################################## > ensmart <- useMart("ensembl_mart_37",dataset="hsapiens_gene_ensembl",mysql=TRUE,a rchive=TRUE) Loading required package: RMySQL Loading required package: DBI connected to: ensembl_mart_37 Reading database configuration of: hsapiens_gene_ensembl Checking attributes and filters ... ok Checking main tables ... ok > gene.list <- getBM(c("entrezgene","chr_name"), filters="chr_name",values=1, mart=ensmart) > gene.list.x <- getBM(c("entrezgene","chr_name","hsapiens_gene_ensembl_structure.5utr_ start"), filters="entrezgene",values= gene.list[,1], mart=ensmart) Error in queryGenerator(attributes = attributes, filter = filters, values = values, : attribute: hsapiens_gene_ensembl_structure.5utr_start is not retrievable via BioMart in MySQL mode, please perform query in the default web service mode ##################################################### Marco On 6/29/07, Durinck, Steffen (NIH/NCI) [F] < durincks at mail.nih.gov> wrote: > > Hi Marco, James, > > Thank you for reporting this. It looks indeed like something goes wrong > when using getFeature with biomaRt in MySQL mode, I'll investigate what > causes this and provide a fix as soon as possible. Part of the error is due > to different naming of the attributes in different versions of Ensembl this > results in the failure of getFeature when used on ensembl_mart_37 > > However I would recommend you to use the more generic getBM function, > which doesn't contain hardcoded attribute/filter names (and thus works with > any Ensembl version), you should be able to get the data as follows: > > ensmart <- > useMart("ensembl_mart_37",dataset="hsapiens_gene_ensembl",mysql=TRUE ,archive=TRUE) > gene.list = getBM(c("entrezgene","chr_name"), filters="chr_name",values=1, > mart=ensmart) > > > gene.list[3:8,] > entrezgene chr_name > 3 441866 1 > 4 81399 1 > 5 135896 1 > 6 26683 1 > 7 79854 1 > 8 148398 1 > > Cheers, > Steffen > > -----Original Message----- > From: James W. MacDonald [mailto:jmacdon at med.umich.edu] > Sent: Thu 6/28/2007 11:55 AM > To: marco zucchelli > Cc: Durinck, Steffen (NIH/NCI) [F]; bioconductor > Subject: Re: [BioC] Biomart with human genes NCBI 35 > > Hi Marco, > > marco zucchelli wrote: > > Dear James and Steffen, > > > > thanks , workks properly now. At the same time seems that the functions > > defined in biomaRt do not work on > > the archived versions. > > Actually, your code doesn't work with the MySQL interface regardless of > the dataset. Although, interestingly enough the error message is > different depending on what dataset you use. > > > mart <- useMart("ensembl","hsapiens_gene_ensembl", mysql=T) > Loading required package: RMySQL > Loading required package: DBI > connected to: ensembl > Reading database configuration of: hsapiens_gene_ensembl > Checking attributes and filters ... ok > Checking main tables ... ok > > > gene.list <- getFeature(chromosome=1, type="entrezgene", mart=mart) > Error in queryGenerator(attributes = attributes, filter = filters, > values = values, : > 'length(filter)' must be 1 when using biomaRt in MySQL mode. > > ensmart <- useMart("ensembl_mart_37",dataset="hsapiens_gene_ensembl", > mysql=TRUE,archive=TRUE) > connected to: ensembl_mart_37 > Reading database configuration of: hsapiens_gene_ensembl > Checking attributes and filters ... ok > Checking main tables ... ok > > gene.list <- getFeature(chromosome=1, type="entrezgene", mart=ensmart) > Error in getFeature(chromosome = 1, type = "entrezgene", mart = ensmart) : > This function only works when using to ensembl. To use this > function > use: mart = useMart('ensembl') > > ## This works > > > cmart <- useMart("ensembl", "hsapiens_gene_ensembl") > Checking attributes and filters ... ok > > gene.list <- getFeature(chromosome=1, type="entrezgene", mart=cmart) > > gene.list > chromosome_name entrezgene > 1 1 79501 > 2 1 26683 > 3 1 81399 > 4 1 729759 > > This looks like something for Steffen. > > Best, > > Jim > > > > > ####### > >> ensmart <- > > > useMart("ensembl_mart_37",dataset="hsapiens_gene_ensembl",mysql=TRUE ,archive=TRUE) > > > > connected to: ensembl_mart_37 > > Reading database configuration of: hsapiens_gene_ensembl > > Checking attributes and filters ... ok > > Checking main tables ... ok > >> gene.list <- getFeature(chromosome=1,type="entrezgene", > > mart=ensmart) > > Error in getFeature(chromosome = 1, type = "entrezgene", mart = ensmart) > : > > This function only works when using to ensembl. To use this function > > use: mart = useMart('ensembl') > > ######## > > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not > be used for urgent or sensitive issues. > >