great!!! this sounds nice, the only thing that i will have to update the local BioMart database frequently :( . Quoting sdurinck@ebi.ac.uk: > Hi Jo, > > You could do a local install of the Ensembl biomart database. Normally > the latest Ensembl release is downloadable from > http://www.ebi.ac.uk/BioMart/install.html > but I am not able to access this right now. If you then change in biomaRt > the host to your local host you should be able to use it. You need to do > this in the package R code but I'll update the package later this week so > you can do this from within R. > > best, > Steffen > >> the biomaRt package is very nice, >> i also downloaded it and tested it, but as i am behind a (****) http >> proxy i am not able to connect to the according servers at ensembl. i >> assume the package connects directly through a SQL connection to the >> database... would it be possible to use a web service? >> >> cheers, jo >> >> Quoting Steffen Durinck <sdurinck@ebi.ac.uk>: >> >>> Hi, >>> >>> You could also try using the biomaRt package (see developmental >>> packages). biomaRt uses direct queries to the latest release of >>> Ensembl to get annotation information. Ensembl does an independent >>> mapping of the affy probe sequences to the genome sequences. This is >>> what I got for your affy id: >>> >>> > library(biomaRt) >>> > mart<-martConnect() >>> - Connected to ensembl_mart_29, ensembl_mart_29, ensembl_mart_29 and >>> ensembl_mart_29 - >>> > getGene(id="208078_s_at",array="hgu133plus2",mart=mart) >>> An object of class "martTable" >>> Slot "id": >>> [1] "208078_s_at" >>> >>> Slot "table": >>> $symbol >>> [1] "SNF1LK" >>> >>> $description >>> [1] "Probable serine/threonine-protein kinase SNF1LK (EC 2.7.1.37). >>> [Source:Uniprot/SWISSPROT;Acc:P57059]" >>> >>> $band >>> [1] "q22.3" >>> >>> $chromosome >>> [1] "21" >>> >>> $start >>> [1] 43658828 >>> >>> $end >>> [1] 43671436 >>> >>> $martID >>> [1] "ENSG00000142178" >>> >>> >>> Cheers, >>> Steffen >>> >>> Dipl.-Ing. Johannes Rainer wrote: >>> >>>> hi, >>>> >>>> i am wondering how the annotation of the Affymetrix chips are >>>> done... i know how the AnnBuilder package works and i also used it, >>>> but as the starting point for any annotation is the GenBank id for >>>> which the probe set codes i would like to know from where this >>>> mapping information comes. are those packages built using the probe >>>> set to genbank mapping that can be downloaded from affymetrix, or >>>> the (sometimes) newer annotation that is available through >>>> Affymetrix NetAffx or some other source? >>>> >>>> I am really interested in this, because we got a little annotation >>>> problem with the annotation for the hgu133plus2 chip (version >>>> 1.7.0). one of our interesting genes in our study was the probe set >>>> 208078_s_at which is mapped using the hgu133plus2 package (and the >>>> annotation from Affymetrix) to NM_030751 (TCF8). we made real time >>>> PCR to confirm its regulation but this TCF8 was not regulated at >>>> all. so i went back to NetAffx tool and saw that Affymetrix gave a >>>> new annotation for this probe set, all 11 probes perfectly match >>>> with the gene NM_173354 (SNF1LK) (i wonder how Affymetrix could >>>> annotate this gene to the TCF8 gene). >>>> >>>> if the annotation packages are built using the downloadable probe >>>> set to genbank mapping files from Affymetrix (which may never >>>> updated and corrected for errors by Affymetrix) i believe that there >>>> may be more annotation errors in this package like the one we found. >>>> >>>> cheers, jo >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> >>> >>> >> >> >> >> > >