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


	[[alternative HTML version deleted]]

