[BioC] biomaRt/martservice query error

[Steve Lianoglou]

Hi,

Maybe I'm missing something, but everything about the scenario you
describe (especially since you are getting errors via their website)
seems to suggest that this is a problem on the biomart side, right?

Perhaps you should try contacting them to let them now?

Sorry if I misunderstood.
-steve

On Wed, Feb 2, 2011 at 3:03 AM, Ying Zhu <Ying.Zhu at csiro.au> wrote:
> Dear Folks,
>
> I encountered a problem with Biomart Query via getBM function in biomaRt package.
>
>>mart <- useMart("plant_mart_7")
> +mart<-useDataset("vvinifera_eg_gene",mart)
> +getBM(attributes=c("affy_vitis_vinifera","go_molecular_function_id","entrezgene"),filters="affy_grape", +values=c("1616932_at","1608265_at","1614550_at","1608133_at","1618459_at"), mart=mart)
> Checking attributes ... ok
> Checking filters ... ok
> Error in getBM(attributes = c("affy_vitis_vinifera", "go_molecular_function_id",  :
>  Query ERROR: caught BioMart::Exception::Database: Error during query execution: Table 'plant_mart_7.efg_affy_vitis_vinifera__dm' doesn't exist
>
> And it's the same error when using web query of http://www.biomart.org/biomart/marview/
>
> Serious Error: Error during query execution: Table 'plant_mart_7.efg_affy_vitis_vinifera__dm' doesn't exist
> ERROR: caught BioMart::Exception::Database: Error during query execution: Table 'plant_mart_7.efg_affy_vitis_vinifera__dm' doesn't exist
>
> I checked this configuration page: http://www.biomart.org/biomart/martservice?type=configuration&dataset=vvinifera_eg_gene
> Two different parameters were found, and I reckon the first was wrong.
> tableConstraint="efg_affy_vitis_vinifera__dm"
> tableConstraint="vvinifera_eg_gene__efg_affy_vitis_vinifera__dm"
> It's obvious that the error happened in "martservice" web server.
> As the file is on the www.biomat.org server, is it possible to fix that within biomaRt package in R?
> Or what do you think is the root problem? I might be wrong to some extent.
> Thanks a lot in advance for anyone could be of kind help and make any suggestions.
> ===================================================
> Cordially yours,
> Ying Zhu
> PostDoctoral Fellow, CSIRO Plant Industry, Adelaide Laboratory
> Wine Innovation West Building, Hartley Grove, Urrbrae SA
> PO Box 350, Glen Osmond SA 5064, Australia
> Facsimile:   +61 8 8303 8601
> Cellphone: +61 4 0121 3248
>
>
>        [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact