[BioC] biomaRt : multiple entrezgene ids to one affy id?

[Steffen Durinck]

Hi Weiwei,

In my previous mail I forgot to mention that Ensembl does and 
independent mapping of the Affymetrix probes to the genomes and if they 
find multiple gene matches for one affy probe then they will display all 
of the matching genes.

Best,
Steffen

Weiwei Shi wrote:
> Dear all:
>
> Here is some piece of output from my query:
>
>   
>> mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
>>     
> Checking attributes and filters ... ok
>
>   
>> getBM(attributes=c("affy_hg_u95a", "entrezgene","ensembl_transcript_id"), filters="affy_hg_u95a", values="31330_at", mart=mart)
>>     
>   affy_hg_u95a entrezgene ensembl_transcript_id
> 1     31330_at       6223       ENST00000221975
> 2     31330_at     728953       ENST00000221975
> 3     31330_at     731572       ENST00000221975
>
> I do not understand why there are multiple entrezgene ids
> corresponding to one affy id. Did I miss something here?
>
> Thanks,
>
>   


-- 
Steffen Durinck, Ph.D.

Oncogenomics Section
Pediatric Oncology Branch
National Cancer Institute, National Institutes of Health
URL: http://home.ccr.cancer.gov/oncology/oncogenomics/

Phone: 301-402-8103
Address:
Advanced Technology Center,
8717 Grovemont Circle
Gaithersburg, MD 20877