Hi Sebastien:

    I suggest you can blat the sequences of probes with no corresponding 
gene symbols to the genome to see if they are sequenced matched to any 
of the genes. That might give you a clue of which genes these probes are 
interrogating.

    Hope this helps.

Cheers,
Wei

Sebastien Gerega wrote:
> Sebastien Gerega <seb@...> writes:
>
>   
>> Hi,
>> I am using the lumi package to analyse illumina microarray data.
>> When it finally comes to getting the top 10 DE genes with topTable I get 
>> many hits with
>> the geneSymbol <NA>. However, if I look up the ProbeID corresponding to 
>> the nuID
>> that provide <NA>, I find that they do correspond to genes. Why aren't 
>> they being
>> displayed in the topTable?
>> thanks,
>> Sebastien
>>
>>                       ID geneSymbol     logFC         t      P.Value    
>> adj.P.Val        B
>> 1917  fwfUovXT3rjAjqbpJU     S100A8 -5.307223 -50.43759 9.854174e-09 
>> 0.0001383625 8.724832
>> 12632 Qd_S7V4OkLjsX3jkt4      KRT6B -5.281406 -39.54237 3.896317e-08 
>> 0.0002735409 8.229157
>> 12149 BjSTT6BOqGLhpKKFGI       <NA> -3.118669 -30.01505 1.844180e-07 
>> 0.0008631377 7.451766
>> 7474  6ipCUUDxcp4ryIj6Uk       <NA> -3.155916 -24.45685 5.835502e-07 
>> 0.0013366890 6.716048
>> 3831  3nivfFfvk55Rd18lLk       <NA> -2.690362 -24.10891 6.324511e-07 
>> 0.0013366890 6.659617
>>
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>>     
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>   
>>     
>
>
> I have looked into this problem a little more...
>
> I downloaded the Human6_v2_sequence spreadsheet from the Illumina
> website and found that many of the targets that provide NA as
> gene symbol have no symbol in the Illumina database either.
>
> For example:
>
> 	ID	geneSymbol
> 5903	ILMN_21212	FAM43A
> 3103	ILMN_1425	FOXO4
> 11993	ILMN_6504	PPL
> 5153	ILMN_19390	ST3GAL4
> 1723	ILMN_12716	CREB3L2
> 4484	ILMN_17676	TNS3
> 2700	ILMN_138461	<NA>
> 1358	ILMN_12133	FSCN1
> 3507	ILMN_15271	CITED4
> 12401	ILMN_73087	<NA>
>
> ILMN_73087 provides NA as gene symbol and does not have a gene
> symbol in the Illumina DB either.
>
> However, ILMN_138461 provides NA as gene symbol but does have a
> gene symbol in the Illumina DB. It is APM-1.
>
> In addition ILMN_73087 has no entries in either the
> Illumina or BioC DB but when I do a search for ILMN_73087 in
> Ensembl I a hit that has multiple EntrezGene listings.
>
> Is there any fix for the NA entries? Is this problem being addressed?
> thanks,
> Sebastien
>
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