Problem solved, Thank you Steffen. Ana. -----Original Message----- From: steffen@stat.Berkeley.EDU [mailto:steffen@stat.Berkeley.EDU] Sent: woensdag 28 januari 2009 6:38 To: Vinuela, Ana Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Error in BioMart and wormbase Dear Ana, It looks like there is a problem with the XML configuration file for that dataset. If you upgrade to using the dev version of biomaRt (http://bioconductor.org/packages/2.4/bioc/html/biomaRt.html) you should be fine for this dataset, as that version does not depend on this XML file anymore. worbase_gene works for me see below: > library(biomaRt) > > wormbase = useMart("wormbase_current", dataset = "wormbase_gene") Checking attributes ... ok Checking filters ... ok > > att = listAttributes(wormbase) > att[1:10,] name description 1 species Species 2 gene Gene WB ID 3 sequence_name Sequence Name (Gene) 4 public_name Gene Public Name 5 cds Sequence Name (CDS) 6 cgc_name Gene CGC Name 7 transcript Sequence Name (Transcript) 8 name_dmlist Gene Names (merged) 9 cds_dmlist Sequence Names (CDS) (merged) 10 transcript_dmlist Sequence Names (Transcript) (merged) > sessionInfo() \R version 2.8.0 (2008-10-20) powerpc-apple-darwin8.11.1 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_1.99.4 loaded via a namespace (and not attached): [1] RCurl_0.92-0 XML_1.98-1 > > Dear all, > > I've been experience a problem with BioMart when I tried to access > wormbase. I am getting an error when I tried to use a specific dataset > (wormbase_gene). This problem do not exist when I access any other > dataset from wormbase. Besides, few months ago a used this code > without problems. > > >> library(biomaRt) >> wormbase = useMart("wormbase_current", dataset = "wormbase_gene") > Checking attributes and filters ...Error in if (xmlGetAttr(xml, > "displayType") == "list" && type != "boolean") options = > parseOptions(xml) : > missing value where TRUE/FALSE needed > >> listDatasets(wormbase) > dataset description version > 1 wormbase_paper Paper > 2 wormbase_gene Gene > 3 wormbase_anatomy_term Anatomy Term > 4 wormbase_expr_pattern Expression Pattern > 5 wormbase_go_term GO Term > 6 wormbase_rnai RNAi > 7 wormbase_phenotype Phenotype > 8 wormbase_variation Variation > >> wormbase = useMart("wormbase_current", dataset = "wormbase_paper") > Checking attributes and filters ... Ok > > > > I will appreciate any help. > > Ana. > > > ############################## >> sessionInfo() > R version 2.8.0 (2008-10-20) > i386-pc-mingw32 > > locale: > LC_COLLATE=Dutch_Netherlands.1252;LC_CTYPE=Dutch_Netherlands.1252;LC_M > ON > ETARY=Dutch_Netherlands.1252;LC_NUMERIC=C;LC_TIME=Dutch_Netherlands.12 > 52 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > other attached packages: > [1] biomaRt_1.16.0 > > loaded via a namespace (and not attached): > [1] RCurl_0.91-0 XML_1.94-0.1 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >