[BioMart Users] Using biomaRt R-package to map probes to ENSEMBL IDs

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[BioMart Users] Using biomaRt R-package to map probes to ENSEMBL IDs

Janne Seppälä
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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Re: [BioMart Users] Using biomaRt R-package to map probes to ENSEMBL IDs

Steffen Durinck-2
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 [hidden email]  .  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

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users