If you use łProbe_Id˛, then you can use package illuminaMousev1.db  to
convert łProbe_Id˛ to Entrez_Gene_ID.
If you use łnuID˛, then you can use package lumiMouseAll.db  to convert
łnuID˛ to Entrez_Gene_ID.
And then do functional analysis based on Entrez_Gene_ID.

Pan

On 4/14/10 10:32 PM, "Lavinia Gordon" <lavinia.gordon@mcri.edu.au> wrote:

> 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':
> Śgi_7305154_ref_NM_013556.1__205_a_7_0ą,
> ŚIGHD_V00786_Ig_heavy_constant_delta_68ą,
> ŚIGHM_V00818_Ig_heavy_constant_mu_941ą,
> ŚIGHV14S1_X03571$M12813_Ig_heavy_variable_14S1_9ą,
> ŚIGKV12-44_AJ235955_Ig_kappa_variable_12-44_18ą, ŚNM_001009981.1ą,
> ŚNM_001024851.3ą, ŚNM_001033378.1ą, ŚNM_001039154.1ą, ŚNM_007381.2ą,
> ŚNM_007393.1ą, ŚNM_007398.2ą, ŚNM_007415.2ą, ŚNM_007421.1ą, ŚNM_007453.2ą,
> ŚNM_007455.1ą, ŚNM_007469.2ą, ŚNM_007472.1ą, ŚNM_007475.2ą, ŚNM_007494.2ą,
> ŚNM_007529.1ą, ŚNM_007537.1ą, ŚNM_007543.2ą, ŚNM_007552.3ą, ŚNM_007569.1ą,
> ŚNM_007609.1ą, ŚNM_007661.2ą, ŚNM_007669.2ą, ŚNM_007671.2ą, ŚNM_007696.2ą,
> ŚNM_007712.1ą, ŚNM_007714.2ą, ŚNM_007745.2ą, ŚNM_007749.1ą, ŚNM_007753.1ą,
> ŚNM_007754.1ą, ŚNM_007782.1ą, ŚNM_007789.2ą, ŚNM_007790.2ą, ŚNM_007811.1ą,
> ŚNM_007812.1ą, ŚNM_007850.1ą, ŚNM_007861.2ą, ŚNM_007862.2ą, ŚNM_007879.1ą,
> ŚNM_007895.2ą, ŚNM_007899.1ą, ŚNM_007907.1ą, ŚNM_007923.1ą, ŚNM_007941.1ą,
> ŚNM_007944.1ą, ŚNM_007948.1ą, ŚNM_007949.2ą, Ś [... 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"
>> <mailto:bioconductor-request@stat.math.ethz.ch>
>> <bioconductor-request@stat.math.ethz.ch>
>> <mailto: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>
>>> <mailto: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> <mailto: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/Catego
>>> ry
>>> .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.


--
Pan Du, PhD
Research Assistant Professor
Northwestern University Biomedical Informatics Center
750 N. Lake Shore Drive, 11-176
Chicago, IL  60611
Office (312) 503-2360; Fax: (312) 503-5388
dupan (at) northwestern.edu

 



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