Hello, I retrieved some attributes from the ensembl database using biomaRt, but I get an error when trying to perform sql commands with sqldf. My code: **** library(biomaRt) library(sqldf) mart <- useMart("ensembl") ensembl <- useMart("ensembl",dataset="hsapiens_gene_ensembl") gene.data <- getBM(attributes=c('go_id','hgnc_symbol', 'ensembl_transcript_id'), filters = 'go_id', values = "GO:0001771", mart = ensembl) gene.data_s <- sqldf("select distinct * from gene.data order by go_id, hgnc_symbol") **** output: > Error in sqliteExecStatement(con, statement, bind.data) : > RS-DBI driver: (error in statement: no such table: gene.data) -- output of sessionInfo(): R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel tcltk stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.12.1 stringr_0.6.2 data.table_1.9.2 biomaRt_2.18.0 [5] GO.db_2.10.1 AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 [9] sqldf_0.4-7.1 RSQLite.extfuns_0.0.1 RSQLite_0.11.4 DBI_0.2-7 [13] gsubfn_0.6-5 proto_0.3-10 loaded via a namespace (and not attached): [1] chron_2.3-45 IRanges_1.20.7 plyr_1.8.1 Rcpp_0.11.1 RCurl_1.95-4.1 reshape2_1.4 stats4_3.0.2 [8] tools_3.0.2 XML_3.95-0.2 -- Sent via the guest posting facility at bioconductor.org.

Hi David, The error has to do with sqldf, which is a CRAN package, rather than biomaRt. Because of that, you should be asking this question on R-help (r-help at r-project.org) rather than this listserv. Best, Jim On 5/6/2014 5:17 AM, David [guest] wrote: > Hello, > > I retrieved some attributes from the ensembl database using biomaRt, but I get an error when trying to perform sql commands with sqldf. > > My code: > **** > library(biomaRt) > library(sqldf) > > mart <- useMart("ensembl") > ensembl <- useMart("ensembl",dataset="hsapiens_gene_ensembl") > > gene.data <- getBM(attributes=c('go_id','hgnc_symbol', 'ensembl_transcript_id'), > filters = 'go_id', values = "GO:0001771", mart = ensembl) > > gene.data_s <- sqldf("select distinct * from gene.data order by go_id, hgnc_symbol") > **** > > output: > >> Error in sqliteExecStatement(con, statement, bind.data) : >> RS-DBI driver: (error in statement: no such table: gene.data) > > > -- output of sessionInfo(): > > R version 3.0.2 (2013-09-25) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel tcltk stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.12.1 stringr_0.6.2 data.table_1.9.2 biomaRt_2.18.0 > [5] GO.db_2.10.1 AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 > [9] sqldf_0.4-7.1 RSQLite.extfuns_0.0.1 RSQLite_0.11.4 DBI_0.2-7 > [13] gsubfn_0.6-5 proto_0.3-10 > > loaded via a namespace (and not attached): > [1] chron_2.3-45 IRanges_1.20.7 plyr_1.8.1 Rcpp_0.11.1 RCurl_1.95-4.1 reshape2_1.4 stats4_3.0.2 > [8] tools_3.0.2 XML_3.95-0.2 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099