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","F54D1 1.1" ) > > getBM (attributes=c > ("wormbase_gene","go_description"),filter="wormbase_gene",values=wor mids > ,mart=mart)->gobiomart > Error: ncol(result) == length(attributes) is not TRUE > > > > Thank you very much > Giovanni > > > debug(getBM) > [...] > Browse[1]> > debug: xmlQuery = paste(" DOCTYPE Query><query virtualschemaname="default" count="0"> > <dataset name="", &gt; 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