Hi Pan,

Thank you for your suggestion.
This is helpful as it provides me with several alternative ids:

 >head(IlluminaIDs)
           Search_Key                              ILMN_Gene       
Accession     Symbol          Probe_Id
580022    "scl29691.6.1_260"                      "0610005I04"    
"NM_177579.2" "0610005I04"    "ILMN_1238136"
2940601   "NM_025791.1"                           "0610006I08RIK" 
"NM_025791.1" "0610006I08Rik" "ILMN_2721178"
102260551 "scl00381629.1_255"                     "0610007C21RIK" 
"NM_212470.2" "0610007C21Rik" "ILMN_1230777"
102370333 "XM_355589.1"                           "0610007C21RIK" 
"NM_212470.2" "0610007C21Rik" "ILMN_2537239"
105670398 "ri|0610007J10|R000001F05|AK018717|633" "0610007J10RIK" 
"AK018717"    "0610007J10Rik" "ILMN_1246069"
102030278 "scl27163.9.1_177"                      "0610007L01RIK" 
"XM_355643"   "0610007L01Rik" "ILMN_2524361"
           Array_Address_Id nuID
580022    "580022"         "6n3oyiKoz7Pj0VTfu0"
2940601   "2940601"        "ZhdXp75JftSF3iWLF4"
102260551 "102260551"      "BRRdqrfuhH69KLodsc"
102370333 "102370333"      "omRXTc0LVpTtklCCPw"
105670398 "105670398"      "upNer6bJTpt27XeZe4"
102030278 "102030278"      "ooevXuTfR0trfSs0RE"

However I cannot use 'Search_Key' as it is non-unique:
 > featureNames(x.snorm.fa) <- IlluminaIDs[,1]
Error in `row.names<-.data.frame`(`*tmp*`, value = c("scl29691.6.1_260",  :
   duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique values when setting 'row.names': 
'gi_7305154_ref_NM_013556.1__205_a_7_0', 
'IGHD_V00786_Ig_heavy_constant_delta_68', 
'IGHM_V00818_Ig_heavy_constant_mu_941', 
'IGHV14S1_X03571$M12813_Ig_heavy_variable_14S1_9', 
'IGKV12-44_AJ235955_Ig_kappa_variable_12-44_18', 'NM_001009981.1', 
'NM_001024851.3', 'NM_001033378.1', 'NM_001039154.1', 'NM_007381.2', 
'NM_007393.1', 'NM_007398.2', 'NM_007415.2', 'NM_007421.1', 
'NM_007453.2', 'NM_007455.1', 'NM_007469.2', 'NM_007472.1', 
'NM_007475.2', 'NM_007494.2', 'NM_007529.1', 'NM_007537.1', 
'NM_007543.2', 'NM_007552.3', 'NM_007569.1', 'NM_007609.1', 
'NM_007661.2', 'NM_007669.2', 'NM_007671.2', 'NM_007696.2', 
'NM_007712.1', 'NM_007714.2', 'NM_007745.2', 'NM_007749.1', 
'NM_007753.1', 'NM_007754.1', 'NM_007782.1', 'NM_007789.2', 
'NM_007790.2', 'NM_007811.1', 'NM_007812.1', 'NM_007850.1', 
'NM_007861.2', 'NM_007862.2', 'NM_007879.1', 'NM_007895.2', 
'NM_007899.1', 'NM_007907.1', 'NM_007923.1', 'NM_007941.1', 
'NM_007944.1', 'NM_007948.1', 'NM_007949.2', ' [... truncated]

which means that I can only use 'Probe_Id', which isn't successful as no 
Illumina annotation packages use Probe_Id as the key.
Any help appreciated.

with regards

Lavinia Gordon.


On 15/04/2010 7:19 AM, Pan Du wrote:
> Hi Lavinia
>
> Illumina Array_Address_Ids is not the regular IDs used in public. You need
> to first convert Array_Address_Ids as Illumina ID or directly convert as
> Entrez Gene IDs, and then do functional analysis.
>
> You can use lumiMouseIDMapping for ID mapping. Here is some code:
>   # convert Array_Address_Ids to nuID first
>   nuIDs = IlluminaID2nuID(addressIDs, lib='lumiMouseIDMapping')
>   # then convert back to regular IlluminaID
>   IlluminaIDs = nuID2IlluminaID(nuIDs, lib='lumiMouseIDMapping')
>   # or map to Entrez ID based on Illumina manifest file (this might be old)
>   entrezIDs = nuID2EntrezID(nuIDs, lib='lumiMouseIDMapping')
>
>
>
> Pan
>
> On 4/14/10 5:00 AM, "bioconductor-request@stat.math.ethz.ch"
> <bioconductor-request@stat.math.ethz.ch>  wrote:
>
>    
>> Message: 21
>> Date: Wed, 14 Apr 2010 15:25:44 +1000
>> From: Lavinia Gordon<lavinia.gordon@mcri.edu.au>
>> To: bioconductor@stat.math.ethz.ch
>> Subject: [BioC] genefilter findLargest and Illumina ids
>> Message-ID:<4BC551D8.60909@mcri.edu.au>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> Dear All
>>
>> I am trying to replicate the example from the Category vignette, but
>> with Illumina data
>> (e.g. from
>> http://bioconductor.org/packages/2.5/bioc/vignettes/Category/inst/doc/Category
>> .R)
>>
>> My data is MouseWG-6_V1
>> where the featureNames(mydata) are Array_Address_Ids (with the data read
>> in as a LumiBatch/ExpressionSet object)
>> and it is BeadStudio output.
>>
>> Using the annotation package illuminaMousev1BeadID.db gives:
>>      
>>> fL = findLargest(featureNames(mydata), abs(ttests$statistic),
>>>        
>> "illuminaMousev1BeadID")
>> Loading required package: org.Mm.eg.db
>> Error in .checkKeys(value, Lkeys(x), x@ifnotfound) :
>>     value for "580022" not found
>>
>> How can I confirm which annotation package to use, as I have BeadStudio
>> data but with Array_Address_Ids?
>> I assume it would be possible to substitute featureNames for
>> featureData, where
>>      
>>> head(featureData(mydata)[[2]])
>>>        
>> [1] "0610005I04"    "0610006I08RIK" "0610007C21RIK" "0610007C21RIK"
>> "0610007J10RIK" "0610007L01RIK"
>> but I haven't had any success in matching these to available keys.
>>
>> Any advice greatly appreciated.
>>
>> with regards
>>
>> Lavinia Gordon.
>>
>> -- 
>> Senior Bioinformatics Officer
>> Murdoch Childrens Research Institute
>> Royal Children's Hospital
>> Flemington Road
>> Parkville
>> Victoria 3052
>> Australia
>> www.mcri.edu.au
>>      
>
>
>
>    


-- 
Senior Bioinformatics Officer
Murdoch Childrens Research Institute
Royal Children's Hospital
Flemington Road
Parkville
Victoria 3052
Australia
www.mcri.edu.au


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