Dear all,

My apologies, the annotation problem was not with biomaRt, but with  
the prepackaged datasets:

1. lumiHumanIDMapping.db and
2. lumiMouseIDMapping.db.

The description of the problem remains the same, though.

Gioulietta and Wolfgang, thank you for the prompt reply.

Regards,

Nenad

p.s. The missing sessionInfo():

R version 2.8.0 (2008-10-20)
i386-apple-darwin8.11.1

locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices datasets  tools     utils     methods
[8] base

other attached packages:
  [1] lumiMouseIDMapping.db_1.0.0 lumiHumanIDMapping.db_1.0.0
  [3] lumi_1.8.3                  RSQLite_0.7-1
  [5] preprocessCore_1.4.0        mgcv_1.4-1.1
  [7] affy_1.20.2                 annotate_1.20.1
  [9] xtable_1.5-4                AnnotationDbi_1.4.2
[11] RMySQL_0.7-2                DBI_0.2-4
[13] biomaRt_1.16.0              R.utils_1.1.1
[15] R.oo_1.4.6                  R.methodsS3_1.0.3
[17] Biobase_2.2.1

loaded via a namespace (and not attached):
[1] RCurl_0.94-0  XML_1.99-0    affyio_1.10.1




>> Hi Nenad,
>>
>> I had a look at our BioMart interface- the web interface at:
>>
>> www.ensembl.org/biomart/martview
>>
>> It appears to me that the Illumina V1 probe set attribute for mouse
>> gives the correct probe names.  I believe the Illumina V1 set for  
>> mouse
>> is the same as MouseWG6_V1.
>>
>> If you give me more details (i.e. which genes you are looking at, or
>> which filters you applied) I can give this another try.  At first
>> glance, it doesn't look like an Ensembl data problem.
>>
>> Regards,
>> Giulietta (Ensembl Helpdesk)
>>
>>
>> On Tue Feb 17 13:35:57 2009, huber@ebi.ac.uk wrote:
>>> 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@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@ebi.ac.uk>
>>> To: bioconductor@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
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor@stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>>

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