[BioC] biomaRt inconsistency: a missing annotation causes a failed query

[Steffen Durinck]

Hi Nenad,

Thanks for reporting this.  It looks like the BioMart web-interface at
www.ensembl.org/biomart produces the same error.  So the error is
upstream of the biomaRt package.  I'll contact the ensembl helpdesk to
make them aware of this issue and we can have a fix soon.

Cheers,
Steffen

On 4/28/10, Nenad Bartonicek <nenad at ebi.ac.uk> wrote:
> Hello,
>
> For some reason, biomaRt is sometimes misbehaving when the query
> results have empty fields. Without returning NA, it fails the whole
> query.
>
>  >library(biomaRt)
>  >ensembl = useMart("ensembl", dataset="mmusculus_gene_ensembl")
>
> #if I ask for an entrezgene id, it does not work
>  >
> getBM
> (attributes
> =
> c
> ("ensembl_transcript_id
> ","entrezgene","description"),filters="ensembl_transcript_id",
> values="ENSMUST00000005400", mart=ensembl)
>
> [1] ensembl_transcript_id entrezgene            description
> <0 rows> (or 0-length row.names)
>
> #if I leave out the entrezgene field, it works
>  >
> getBM
> (attributes
> =
> c
> ("ensembl_transcript_id
> ","description"),filters="ensembl_transcript_id",
> values="ENSMUST00000005400", mart=ensembl)
>
> ensembl_transcript_id
> 1    ENSMUST00000005400
>                                                  description
> 1 prolactin receptor Gene [Source:MGI Symbol;Acc:MGI:97763]
>
>  > sessionInfo()
> R version 2.11.0 (2010-04-22)
> i386-apple-darwin9.8.0
>
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> other attached packages:
> [1] biomaRt_2.4.0     R.utils_1.4.0     R.oo_1.7.2
> R.methodsS3_1.2.0
> [5] Biobase_2.7.4
>
> loaded via a namespace (and not attached):
> [1] affy_1.25.2          affyio_1.15.2        limma_3.3.10
> [4] marray_1.25.1        preprocessCore_1.9.0 RCurl_1.3-1
> [7] tools_2.11.0         XML_2.8-1
>
>
> Does anyone have an idea why this might be hapening?
>
> Cheers,
>
> Nenad Bartonicek
>
> Nenad Bartonicek
> PhD student, Enright group
> European Bioinformatics Institute
> Hinxton
> Cambridge
> CB10 1SD
> United Kingdom
> tel: +44-755-435-9057
>
>
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>
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