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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