[BioC] getBM (biomaRt) sometimes returns NULL

[Giovanni Coppola]

Hello Wolfgang,
I am actually getting a different error now... the wormids list is  
usually much longer.

 > wormids<-c("ZK666.6","Y41C4A. 
11","T02G5.7.1","K08F4.7","A_12_P11025","ZC410.5b","C32H11.2","F54D11.1" 
)
 > getBM (attributes=c 
("wormbase_gene","go_description"),filter="wormbase_gene",values=wormids 
,mart=mart)->gobiomart
Error: ncol(result) == length(attributes) is not TRUE
 >

Thank you very much
Giovanni


debug(getBM)
[...]
Browse[1]>
debug: xmlQuery = paste("<?xml version='1.0' encoding='UTF-8'?><! 
DOCTYPE Query><Query  virtualSchemaName = 'default' count = '0'>  
<Dataset name = '",
     mart at dataset, "'>", sep = "")
Browse[1]>
debug: attributeXML = paste("<Attribute name = '", attributes, "'/>",
     collapse = "", sep = "")

 > sessionInfo()
R version 2.1.0, 2005-05-12, powerpc-apple-darwin7.9.0

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

other attached packages:
biomaRt    RCurl      XML  convert   marray    limma  Biobase
"1.5.12"  "0.6-1" "0.99-6"  "1.1.7"  "1.6.3"  "2.0.8" "1.5.12"
 >


On Mar 24, 2006, at 10:26 AM, Wolfgang Huber wrote:

> Ciao Giovanni,
>
> can you provide a script that allows us to reproduce this error?
>
> In any case, I think getBM should produce a useful error message  
> rather than just quietly returning NULL and we will fix this.
>
> To be even more helpful, you could also say "debug(getBM)" before  
> calling getBM, and report to us the content of "xmlQuery" and  
> "postRes" after the call to the "postForm" function (this is the  
> main action of the function getBM, when it talks to the Wormbase  
> webservice).
>
> Best wishes
>  Wolfgang
>
>
> -------------------------------------
> Wolfgang Huber
> European Bioinformatics Institute
> European Molecular Biology Laboratory
> Cambridge CB10 1SD
> England
> Phone: +44 1223 494642
> Fax:   +44 1223 494486
> Http:  www.ebi.ac.uk/huber
> -------------------------------------
>
>
> Giovanni Coppola wrote:
>> Hello everybody,
>> I am using biomaRt to retrieve worm annotation.
>> Sometimes (apparently unpredictably) I get a NULL output and a  
>> warning:
>>  > getBM (attributes=c  
>> ("wormbase_gene","go_description"),filter="wormbase_gene",values=worm 
>> ids ,mart=mart)->gobiomart
>> Warning message:
>> getBM returns NULL. in: getBM(attributes = c("wormbase_gene",   
>> "go_description"), filter = "wormbase_gene",
>> The exact same line works later. Has anyone experienced this? Is   
>> there a timeout issue or something like that?
>> Thanks
>> Giovanni
>>  > sessionInfo()
>> R version 2.2.1, 2005-12-20, powerpc-apple-darwin7.9.0
>> attached base packages:
>> [1] "tools"     "methods"   "stats"     "graphics"  "grDevices"  
>> "utils"
>> [7] "datasets"  "base"
>> other attached packages:
>> biomaRt    RCurl      XML  convert   marray    limma  Biobase
>> "1.5.12"  "0.6-0" "0.99-6"  "1.4.0"  "1.8.0"  "2.4.7"  "1.8.0"