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On 8/9/05 12:16 PM, "Jamain, Adrien J" <adrien.jamain at="" imperial.ac.uk=""> wrote: > Dear all, > > I'm totally puzzled by biomaRt this afternoon. I've used it in the past > without problem, and today I can't seem to get any annotation to any > probeset... (see example below) > > Is there something obvious I'm doing wrong? No, it isn't you. Ensembl changed the database structure slightly. BiomaRt will need to be modified slightly to match the newest schema. Sean

Dear Adrien, Which version of biomaRt do you use? You need 1.1.7 or above. As a new version of Ensembl gets released about every 2 months, changes to the Ensmart schema are possible. When their schema changes, we currently have to update biomaRt as well. You can download the latest biomaRt version from the developmental packages. For Windows users note that the version available via the Bioconductor website seems to lack behind on the Linux version. The latest Windows version can also be found here: http://www.esat.kuleuven.ac.be/~sdurinck/ best, Steffen Dear all, I'm totally puzzled by biomaRt this afternoon. I've used it in the past without problem, and today I can't seem to get any annotation to any probeset... (see example below) Is there something obvious I'm doing wrong? Thanks, Adrien PS: The probeset in the example is well annotated in Ensembl, I've checked on the website. >> martDisconnect(mart) [1] TRUE >> mart = martConnect() - Connected to: ensembl_mart_32 - - Connected to: vega_mart_32 - - Connected to: snp_mart_32 - - Connected to: sequence_mart_32 - >> getGene(id = "1415670_at", array = "mouse430_2", mart=mart) An object of class "martTable" Slot "id": [1] "1415670_at" Slot "table": $symbol [1] NA $description [1] NA $band [1] NA $chromosome [1] NA $start [1] NA $end [1] NA $martID [1] NA [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor