Hi Steffen, Thanks for your quick response. I did the upgrade to 1.9.29 and everything works! Thanks very much, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html http://staff.washington.edu/~dbeyer ********************************************************************** ********* On Fri, 20 Apr 2007, Steffen Durinck wrote: > Hi Dick, > > Not sure what's going wrong, try updating to the 1.9.29 devel version of the > package. > I tried your query and have no problems: > > getGO(id=3064,type="entrezgene",mart=mart) > entrezgene go go_description evidence_code > 1 3064 GO:0003714 transcription corepressor activity TAS > 2 3064 GO:0005215 transporter activity TAS > 3 3064 GO:0005515 protein binding IPI > 4 3064 GO:0005625 soluble fraction TAS > 5 3064 GO:0005634 nucleus TAS > .... > > Best regards, > Steffen > > Dick Beyer wrote: >> I'm having difficulty getting biomaRt getGO() to work. Here is a typical >> session: >> >> >>> library(biomaRt) >>> >> >> >>> mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") >>> >> Checking attributes and filters ... ok >> >> >>> g <- getGO(id=3064,type="entrezgene",mart=mart) >>> >> Error: ncol(result) == length(attributes) is not TRUE >> >> >> >>> listDatasets(mart) >>> >> dataset version >> 1 oanatinus_gene_ensembl OANA5 >> 2 gaculeatus_gene_ensembl BROADS1 >> 3 cporcellus_gene_ensembl GUINEAPIG >> 4 lafricana_gene_ensembl BROADE1 >> 5 stridecemlineatus_gene_ensembl SQUIRREL >> 6 scerevisiae_gene_ensembl SGD1.01 >> 7 eeuropaeus_gene_ensembl HEDGEHOG >> 8 etelfairi_gene_ensembl TENREC >> 9 ptroglodytes_gene_ensembl CHIMP2.1 >> 10 cintestinalis_gene_ensembl JGI2 >> 11 ocuniculus_gene_ensembl RABBIT >> 12 hsapiens_gene_ensembl NCBI36 >> 13 ggallus_gene_ensembl WASHUC2 >> 14 tbelangeri_gene_ensembl TREESHREW >> 15 tnigroviridis_gene_ensembl TETRAODON7 >> 16 mmulatta_gene_ensembl MMUL_1 >> 17 mmusculus_miscfeature NCBIM36 >> 18 olatipes_gene_ensembl MEDAKA1 >> 19 hsapiens_miscfeature NCBI36 >> 20 btaurus_gene_ensembl Btau_3.1 >> 21 aaegypti_gene_ensembl AaegL1 >> 22 csavignyi_gene_ensembl CSAV2.0 >> 23 rnorvegicus_gene_ensembl RGSC3.4 >> 24 fcatus_gene_ensembl CAT >> 25 celegans_gene_ensembl WB170 >> 26 trubripes_gene_ensembl FUGU4 >> 27 agambiae_miscfeature AgamP3 >> 28 dnovemcinctus_gene_ensembl ARMA >> 29 agambiae_gene_ensembl AgamP3 >> 30 mlucifugus_gene_ensembl MICROBAT1 >> 31 xtropicalis_gene_ensembl JGI4.1 >> 32 drerio_gene_ensembl ZFISH6 >> 33 mdomestica_gene_ensembl BROADO3 >> 34 ogarnettii_gene_ensembl BUSHBABY1 >> 35 dmelanogaster_gene_ensembl BDGP4.3 >> 36 mmusculus_gene_ensembl NCBIM36 >> 37 cfamiliaris_gene_ensembl BROADD2 >> >> sessionInfo() >> R version 2.4.1 (2006-12-18) i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" >> "methods" "base" >> >> other attached packages: >> biomaRt RCurl XML Rgraphviz geneplotter graph >> annotate Biobase GO >> "1.8.2" "0.8-0" "1.1-1" "1.12.1" "1.12.0" "1.12.0" >> "1.12.0" "1.12.2" "1.14.0" >> >> I tried many variations of arguments to getGO and getGene. I tried the >> examples in the help, but still got the same error. >> >> If anyone had some suggestions, I would be most grateful. >> >> Thanks much, >> Dick >> ******************************************************************* ************ >> Richard P. Beyer, Ph.D. University of Washington >> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >> Seattle, WA 98105-6099 >> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >> http://staff.washington.edu/~dbeyer >> >> _______________________________________________ >> 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 >> > > > -- > Steffen Durinck, Ph.D. > > Oncogenomics Section > Pediatric Oncology Branch > National Cancer Institute, National Institutes of Health > URL: http://home.ccr.cancer.gov/oncology/oncogenomics/ > > Phone: 301-402-8103 > Address: > Advanced Technology Center, > 8717 Grovemont Circle > Gaithersburg, MD 20877 >