[BioC] biomaRt error

Mark Robinson mrobinson at wehi.EDU.AU
Sun Nov 23 05:12:15 CET 2008


Hi Sonia.

I don't know what you have in your 'ids' variable, but this command  
works fine for me on the latest version of R/biomaRt.  I suspect  
updating your version of R/biomaRt is all you need ... see below for  
my commands on a fresh R session.  Also, I think there have been a  
couple minor internal biomart changes in that time.

Cheers,
Mark


------------
 > library(biomaRt)

 > mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
Checking attributes and filters ... ok

 > getBM(attributes=c("ensembl_gene_id","hgnc_symbol","description"),  
filter="ensembl_gene_id", value="ENSG00000060237", mart=mart)
  ensembl_gene_id hgnc_symbol
1 ENSG00000060237        WNK1
                                                                                                                          description
1 Serine/threonine-protein kinase WNK1 (EC 2.7.11.1) (Protein kinase  
with no lysine 1) (Protein kinase, lysine-deficient 1) (Kinase  
deficient protein) (Erythrocyte 65 kDa protein) (p65)  
[Source:UniProtKB/Swiss-Prot;Acc:Q9H4A3]

 > sessionInfo()
R version 2.8.0 (2008-10-20)
i386-apple-darwin8.11.1

locale:
en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomaRt_1.16.0

loaded via a namespace (and not attached):
[1] RCurl_0.91-0 XML_1.98-1
------------




On 21/11/2008, at 9:51 PM, Sonia SHAH wrote:

> Hi
>
> I was carrying out the following biomaRt query:
> getBM(attributes=c("ensembl_gene_id","hgnc_symbol","description"),  
> filter="ensembl_gene_id", value=ids, mart=mart)
>
> and I got the following error:
> 1 Query ERROR: caught BioMart::Exception::Database: Error during  
> query execution: You have an error in your SQL syntax; check the  
> manual that corresponds to your MySQL server version for the right  
> syntax to use near 'AND  
> main.gene_id_1020_key=ensembl_mart_51.hsapiens_gene_ensembl_
> Error in getBM(attributes = c("ensembl_gene_id", "hgnc_symbol",  
> "description"),  :
> Number of columns in the query result doesn't equal number of  
> attributes in query.  This is probably an internal error, please  
> report.
>
> I don't get errors with queries made to the ENSEMBL 51 VARIATION  
> database but get them when using the ENSEMBL 51 GENES database
>
> sessionInfo()
> R version 2.6.1 (2007-11-26)
> x86_64-unknown-linux-gnu
> locale:
> LC_CTYPE 
> = 
> en_GB 
> ;LC_NUMERIC 
> = 
> C 
> ;LC_TIME 
> = 
> en_GB 
> ;LC_COLLATE 
> = 
> en_GB 
> ;LC_MONETARY 
> = 
> en_GB 
> ;LC_MESSAGES 
> = 
> en_GB 
> ;LC_PAPER 
> = 
> en_GB 
> ;LC_NAME 
> = 
> C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB;LC_IDENTIFICATION=C
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] biomaRt_1.14.1 RCurl_0.8-3
> loaded via a namespace (and not attached):
> [1] rcompgen_0.1-17 XML_1.93-2
>
>
>
>
> -- 
> Sonia Shah
> Bloomsbury Centre for Bioinformatics
> Department of Computer Science
> New Engineering Building
> Malet Place
> London WC1E 6BT
>
> _______________________________________________
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------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852



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