Hi Stefanie,

Thank you for reporting this.  The issue is that ENST00000594647 is a
fairly new transcript id that was introduced in Ensembl 70.
By default you do your biomaRt queries to the central BioMart server which
usually is quite good at updating it's Ensembl version whenever there is a
new version of Ensembl (with about a 2 week lag).  However at this time the
BioMart server runs Ensembl 69 and the Ensembl database has had a new
release last month to Ensembl 71.  As ENST00000594647 was introduced in
Ensembl 70 it doesn't return a result in version 69.

Here's how you can query the current Ensembl version and get a result for
this new transcript:
>  ids = c("ENST00000594647","ENST00000335137")
> ensembl = useMart("ENSEMBL_MART_ENSEMBL", dataset =
"hsapiens_gene_ensembl", host="www.ensembl.org")
> getBM(attributes=c("ensembl_transcript_id","external_gene_id"), values =
ids, filters = "ensembl_transcript_id", mart = ensembl)
  ensembl_transcript_id external_gene_id
1       ENST00000335137            OR4F5
2       ENST00000594647       AL627309.2

I will contact the BioMart developers to check what the plan is to update
the BioMart server to the latest version of Ensembl and report this back
 as a reply to this email.

Cheers,
Steffen





On Fri, May 3, 2013 at 5:23 AM, Stefanie Tauber <
stefanie.tauber@univie.ac.at> wrote:

> Dear list,
>
> I would like to retrieve some gene names for some ensembl transcript ids:
>
> library(biomaRt)
>
> > ids = c("ENST00000594647","ENST00000335137")
>
> > getBM(attributes=c("ensembl_transcript_id","external_gene_id"), values =
> ids, filters = "ensembl_transcript_id", mart = useMart("ensembl", dataset =
> "hsapiens_gene_ensembl"))
>
> 1       ENST00000335137            OR4F5
>
>
> Why don't I get a gene name for the first ID, which should be AL627309.2
> according to:
>
>
> http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000268020;r=1:53049-54936;t=ENST00000594647
>
> ?
>
>
> Best regards,
> Stefanie
>
>
> sessionInfo()
> R version 3.0.0 beta (2013-03-24 r62391)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] de_AT.UTF-8/de_AT.UTF-8/de_AT.UTF-8/C/de_AT.UTF-8/de_AT.UTF-8
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] biomaRt_2.15.1          GenomicFeatures_1.11.16 AnnotationDbi_1.21.16
> [4] Biobase_2.19.3          GenomicRanges_1.11.40   IRanges_1.17.41
> [7] BiocGenerics_0.5.6
>
> loaded via a namespace (and not attached):
>  [1] Biostrings_2.27.12  bitops_1.0-5        BSgenome_1.27.1
>  [4] DBI_0.2-5           RCurl_1.95-4.1      Rsamtools_1.11.27
>  [7] RSQLite_0.11.2      rtracklayer_1.19.11 stats4_3.0.0
> [10] tools_3.0.0         XML_3.96-0.2        zlibbioc_1.5.0
> _______________________________________________
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>

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