[BioC] biomaRt error in getGene
georg.otto at tuebingen.mpg.de
Thu Jul 13 16:36:19 CEST 2006
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...
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.
> 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)
>> 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)
>> I tried with several different affymetrix probes that should be
>> annotated in ensembl, but all of them gave me a "NULL"
>> Version 2.3.0 (2006-04-24)
>> attached base packages:
>>  "stats" "graphics" "grDevices" "utils" "datasets" "methods"
>>  "base"
>> other attached packages:
>> biomaRt RCurl XML
>> "1.7.3" "0.6-2" "0.99-7"
>> Any idea what could be wrong here?
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