Hi Janne,
There should be no difference in the results you are getting using the archived version of Ensembl. As biomaRt is not responsible for the content of the database, your question will be best answered by the Ensembl team at [email protected] . Give them the list of ids that you found where different and they can investigate also as a biomaRt user it is helpful if you give them the XML version of your query which you can get by setting verbose=TRUE in your getBM query: ensembl<-getBM(attributes = c("ensembl_gene_id", "illumina_humanwg_6_v2"), mart = mart1, verbose=TRUE) <?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' requestid= "biomaRt"> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Attribute name = 'illumina_humanwg_6_v2'/></Dataset></Query> Cheers, Steffen Hi all, As the subject implies, I have been using the biomaRt R-package to map (Illumina and Agilent) probe identifiers to ENSEMBL gene identifiers in a large-scale database project. On January the 17th I processed a set of Illumina microarray measurements. At that time, biomaRt used Ensembl version 60. Below is the script I used to get the Illumina probeID-to-EnsemblID annotations: mart1<-useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl") ensembl<-getBM(attributes = c("ensembl_gene_id", "illumina_humanwg_6_v2"), mart = mart1) However, when I now try to access the same archived Ensembl version (60), the EnsemblID list differs from the one I created on 17/1/2011 (about 3-5% of the geneIDs are missing or have changed between the lists). I actually tried all Ensembl versions between 58 and 62, but none of them produced an identical ID list to the one I created earlier. Below is the only change I made to the probe annotation part of the script: mart1<-useMart(host = "nov2010.archive.ensembl.org", biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl") It is important in our project to get the EnsemblIDs in the same namespace and to be able to reproduce exactly the same results as before. Has anyone else encountered this issue, or does anyone have any idea what I might have misunderstood or what I am doing wrong here? Any insight is warmly appreciated! Best regards, Janne Seppälä
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