[BioC] getBM (biomaRt) sometimes returns NULL

[Wolfgang Huber]

Dear Giovanni,

can you send us a sufficient code example to reproduce this error 
please? Otherwise nobody can really do anything about your problem.
I.e. how did you obtain your "mart" object?

  Best
  Wolfgang

Giovanni Coppola wrote:
> 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"
> 
> 


-- 
Best regards
   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