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

[Nenad Bartonicek]

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