[BioC] biomaRt error in getGene

[Georg Otto]

Besides "affy_zebrafish" there is also an attribute
"affy_zebrafish_primary_id". Could this have something to do with the
problem, or could I use "affy_zebrafish_primary_id" instead of
"affy_zebrafish"? Sorry for the naive question, but I am not very
familiar with ensembl/biomart...

Cheers,

Georg

Steffen Durinck <durincks at mail.nih.gov> writes:

> Hi Georg,
>
> I've repeated your query and unfortunately get the same error. 
> When using biomaRt with Ensembl,  it should return the same output as 
> the Ensembl BioMart web application (http://www.ensembl.org/Multi/martview).
> I often use this to verify that biomaRt is properly functioning or to 
> find out if the reported error is due to a database error or due to a 
> bug in the biomaRt package.
>
> After doing a query using zebrafish affy ids, the MartView web 
> application also returns no values for affy ids (e.g. querying for all 
> affy ids on zebrafish chromosome 1).
> It looks thus like there is an error in the zebrafish dataset of 
> Ensembl.  Any problems of  this type should be reported at the 
> corresponding database so they can be fixed in the next database 
> release. For Ensembl this is helpdesk at ensembl.org. 
> <mailto:helpdesk at ensembl.org>
> I'll document this in the biomaRt vignette.
>
> Best,
> Steffen
>
>
>
> Georg Otto wrote:
>> Hi Steffen,
>>
>> thanks for your help. I updated to biomaRt 1.7.3 and followed your
>> advice. What I got is this:
>>
>>   
>>> mart <- useMart("ensembl")
>>> mart<-useDataset("drerio_gene_ensembl", mart)
>>>     
>>
>>   
>>> getGene(id="Dr.10336.1.S1_at", array="affy_zebrafish", mart=mart)
>>>     
>> NULL
>>
>> then I tried with getBM
>>
>>   
>>> getBM(attributes=c("ensembl_transcript_id", "affy_zebrafish", "refseq_dna"), filters="affy_zebrafish", values="Dr.10336.1.S1_at", mart=mart)
>>>     
>> NULL
>>
>> I tried with several different affymetrix probes that should be
>> annotated in ensembl, but all of them gave me a "NULL"
>>
>>   
>>> sessionInfo()
>>>     
>> Version 2.3.0 (2006-04-24) 
>> x86_64-redhat-linux-gnu 
>>
>> attached base packages:
>> [1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"  
>> [7] "base"     
>>
>> other attached packages:
>>  biomaRt    RCurl      XML 
>>  "1.7.3"  "0.6-2" "0.99-7" 
>>
>> Any idea what could be wrong here?
>>
>> Best,
>>
>> Georg