Hello Steffen and others, Has the capability of searching older versions of Ensembl been added to the R version of biomaRt yet? Thanks, Lynn Amon

Dear Lynn, Yes it has but it is only available using biomaRt in MySQL mode. Here's how to get access: 1) Check which archives are available library(biomaRt) listMarts(archive=TRUE, mysql=TRUE) this will give the following Ensembl archives 23 ensembl_mart_29 24 ensembl_mart_30 25 ensembl_mart_31 26 ensembl_mart_32 27 ensembl_mart_33 28 ensembl_mart_34 29 ensembl_mart_35 30 ensembl_mart_36 31 ensembl_mart_37 32 ensembl_mart_38 33 ensembl_mart_39 34 ensembl_mart_40 35 ensembl_mart_41 36 ensembl_mart_42 37 ensembl_mart_43 38 ensembl_mart_44 39 ensembl_mart_45 40 ensembl_mart_46 41 ensembl_mart_47 2) Connect to the archive (e.g. let's connect to Ensembl 44): ensembl = useMart("ensembl_mart_44", dataset="hsapiens_gene_ensembl",archive=TRUE, mysql=TRUE) 3) Perform your biomaRt queries as you usually do. I would recommend using the getBM function as this doesn't contain hard-coded attribute and filter names. getGene, getGO etc might fail on older Ensembl versions as attributes might be renamed in the meantime. Cheers, Steffen ----- Original Message ----- From: Lynn Amon <lamon@fhcrc.org> Date: Tuesday, October 23, 2007 3:27 pm Subject: [BioC] are older versions of Ensembl accessible with biomaRt? To: bioconductor at stat.math.ethz.ch > Hello Steffen and others, > Has the capability of searching older versions of Ensembl been > added to > the R version of biomaRt yet? > Thanks, > Lynn Amon > > _______________________________________________ > 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