[BioC] problem with fetching gene information in biomaRt for mouse_430_2

[Cei Abreu-Goodger]

There are always some discrepancies between different databases. Biomart 
takes data from Ensembl, which do their own Affy probe-to-genome 
mapping. The probeset you're looking for isn't mapped to the mouse 
genome, according to Ensembl.

Cei

Edmund Chang wrote:
> Dear List,
> I noticed that for some of the probesets (e.g. 1447625_at), information
> retrieved by biomaRt is NULL. However, Affymetrix has it annotated as "E2F5"
> when I checked on NetAffx. Why is there a discrepancy? Ultimately, I am
> hoping to use biomaRt to find homologs of the mouse probesets on a
> Affymetrix human expression array.
> Any help in clarifying this situation would be greatly appreciated. Thanks!
>
>   
>> library(biomaRt)
>> ensembl <- useMart("ensembl")
>> mouse <- useMart("ensembl", "mmusculus_gene_ensembl")
>> getGene(id="1448859_at", type="affy_mouse430_2", mart =mouse)
>>     
>   affy_mouse430_2 markersymbol
> 1      1448859_at       Cxcl13
>                                                               description
> chromosome_name band
> 1 chemokine (C-X-C motif) ligand 13
> [Source:MarkerSymbol;Acc:MGI:1888499]               5   E3
>   strand start_position end_position    ensembl_gene_id
> ensembl_transcript_id
> 1      1       96197241     96201370 ENSMUSG00000023078
> ENSMUST00000023840
>
>   
>> getGene(id="1447625_at", type="affy_mouse430_2", mart =mouse)
>>     
> NULL
>
> -Ed
> Edmund Chang, PhD
> One Baylor Plaza M635
> Houston, Tx 77030
> 713-798-6217
>
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-- 
Cei Abreu-Goodger, PhD

Wellcome Trust Sanger Institute
Computational and Functional Genomics
Wellcome Trust Genome Campus
Hinxton, Cambridge, CB10 1SA, UK



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