[BioC] problem in biomaRt: getBM(output="list")

[Steffen Durinck]

Hi Georg,

You found a bug and I've fixed it.  The changes have been committed to 
the repository.
(I will send you a new build shortly)

Thanks for reporting this.

best,
Steffen

Georg Otto wrote:
> Hi,
>
> I have encountered a problem in biomaRt which is not serious, but kind
> of annoying...
>
> The atribute "zfin_xpat" (and maybe others) causes an error when the
> output option "list" is chosen.
>
> For example:
>
> library(biomaRt)
> ensembl<-useMart("ensembl", dataset="drerio_gene_ensembl")
>
> # this works:
>
>   
>> getBM(attributes=c("zfin_xpat"), filters="affy_zebrafish", values=c("Dr.12.1.S2_at","Dr.12259.1.S1_at", "Dr.13845.1.A1_at"), mart=ensembl)
>>     
>              zfin_xpat
> 1    ZDB-GENE-031008-1
> 2 ZDB-GENE-040426-1778
> 3 ZDB-GENE-040426-1778
>
>
> # this does not work:
>
>   
>> getBM(attributes=c("zfin_xpat"), filters="affy_zebrafish", values=c("Dr.12.1.S2_at","Dr.12259.1.S1_at", "Dr.13845.1.A1_at"), mart=ensembl, output="list")
>>     
> Error in read.table(con, sep = "\t", header = FALSE, quote = "", comment.char = "",  : 
> 	no lines available in input
>   
>> traceback()
>>     
> 4: stop("no lines available in input")
> 3: read.table(con, sep = "\t", header = FALSE, quote = "", comment.char = "", 
>        as.is = TRUE)
> 2: getBM(attributes = attributes[j], filters = filters, values = values[k], 
>        mart = mart)
> 1: getBM(attributes = c("zfin_xpat"), filters = "affy_zebrafish", 
>        values = c("Dr.12.1.S2_at", "Dr.12259.1.S1_at", "Dr.13845.1.A1_at"), 
>        mart = ensembl, output = "list")
>
>
>   
>> sessionInfo()
>>     
> R version 2.4.0 (2006-10-03) 
> powerpc-apple-darwin8.8.0 
>
> locale:
> C
>
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets" 
> [7] "base"     
>
> other attached packages:
> biomaRt   RCurl     XML 
> "1.8.1" "0.8-0" "1.3-2" 
>
> I think that this problem did not occur in the Ensembl release before
> the current one. Any idea what is going on?
>
> Best,
>
> Georg
>
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>   


-- 
Steffen Durinck, Ph.D.

Oncogenomics Section
Pediatric Oncology Branch
National Cancer Institute, National Institutes of Health
URL: http://home.ccr.cancer.gov/oncology/oncogenomics/

Phone: 301-402-8103
Address:
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8717 Grovemont Circle
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