[BioC] getBM outputs logical(0)

[Stefanie Tauber]

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