[BioC] [Fwd: Reporting problem with annotation in biomaRt, Illumina arrays]

[Wolfgang Huber]

Hi Nenad

thank you for reporting this!

Since your question raises a more general operational question with 
biomaRt, I'd like to use the opportunity to explain, to this list, 
what's going on (not quite) behind the scenes. There are three separate 
organisations involved in this information chain:

1. The Ensembl database team (in Cambridge UK)

2. The BioMart software developers (in Toronto CA) and Rhoda Kinsella 
(in Cambridge) who imports the Ensembl data into the BioMart system

3. Bioconductor and specifically the biomaRt R package, which is simply 
a thin interface from R to a webservice, with no own content or logic 
(maintained Steffen Durinck in sunny Berkeley.)

Questions at levels 2 and 3 are good to ask on this list and are usually 
efficiently answered e.g. by Steffen or Rhoda.

What you report is, afaIct, an Ensembl data content problem, i.e. level 
1. Here the advise is to email the Ensembl help desk: helpdesk at ensembl.org

I hope this helps, please let us know if you have any more questions or 
observations.

Best wishes
      Wolfgang

----------------------------------------------------
Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber
	

-------- Original Message --------
Subject: [BioC] Reporting problem with annotation in biomaRt, Illumina 
arrays
Date: Tue, 17 Feb 2009 12:02:37 +0000
From: Nenad Bartonicek <nenad at ebi.ac.uk>
To: bioconductor at stat.math.ethz.ch

Dear all,

There seems to be a problem with probe annotation of certain Illumina
arrays in biomaRt.

The following arrays: HumanWG6_V1, HumanRef8_V1, MouseWG6_V1,
MouseWG6_V1_B do not have valid Illumina probe names under the
"ProbeId" column.
They seem to contain values which are in the column
"Array_Address_Id", which is the one next to the Probe_id column in
the official Illumina flat files.

For example. the array "MouseWG6_V1"

library(lumiMouseIDMapping.db)
dbconn=lumiMouseIDMapping_dbconn()
tableNames=dbListTables(lumiMouseIDMapping_dbconn())
tableNames = tableNames[grep("Mouse",tableNames)]
tableNames
data = dbReadTable(dbconn,"MouseWG6_V1")
head(data)

The column ProbeId contains identifier "105290026" which is in the
flat file on
http://www.switchtoi.com/pdf/Annotation%20Files/Mouse/MouseWG-6_V1_1_R4_11234304_A.zip
under the column Array_Address_Id and has a proper identifier of
"ILMN_1229450".

Hope this helps and that it might be corrected sometime in the future,

Nenad

Nenad Bartonicek
EMBL- European Bioinfromatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge

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