Dear List, When I tried to run examples in the user guide of package "GenomeGraphs", I got the following error message after coping the code on page 3. The code on page 2 "gdPlot(gene)"works fine. > transcript <- makeTranscript(id = "ENSG00000095203", type = "ensembl_gene_id", biomart = mart) Error in getBM(c("structure_gene_stable_id", "structure_transcript_stable_id", : Invalid attribute(s): structure_gene_stable_id, structure_transcript_stable_id Please use the function 'listAttributes' to get valid attribute names Can anybody kindly tell me what I am missing? Thanks. > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.iso885915;LC_NUMERIC=C;LC_TIME=en_US.iso885915;LC_COLLA TE=en_US.iso885915;LC_MONETARY=C;LC_MESSAGES=en_US.iso885915;LC_PAPER= en_US.iso885915;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=e n_US.iso885915;LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomeGraphs_1.2.3 biomaRt_2.0.0 loaded via a namespace (and not attached): [1] RCurl_0.94-1 XML_2.3-0 -- Xiaoling

Hi Shirley, It looks like your version of GenomeGraphs is too old. Update GenomeGraphs to a version of 1.4.0 or higher and this example should work again. Cheers, Steffen > Dear List, > > When I tried to run examples in the user guide of package > "GenomeGraphs", I got the following error message > after coping the code on page 3. The code on page 2 > "gdPlot(gene)"works fine. > >> transcript <- makeTranscript(id = "ENSG00000095203", type = >> "ensembl_gene_id", biomart = mart) > Error in getBM(c("structure_gene_stable_id", > "structure_transcript_stable_id", : > Invalid attribute(s): structure_gene_stable_id, > structure_transcript_stable_id > Please use the function 'listAttributes' to get valid attribute names > > Can anybody kindly tell me what I am missing? Thanks. > >> sessionInfo() > R version 2.9.0 (2009-04-17) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.iso885915;LC_NUMERIC=C;LC_TIME=en_US.iso885915;LC_COL LATE=en_US.iso885915;LC_MONETARY=C;LC_MESSAGES=en_US.iso885915;LC_PAPE R=en_US.iso885915;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT =en_US.iso885915;LC_IDENTIFICATION=C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] GenomeGraphs_1.2.3 biomaRt_2.0.0 > > loaded via a namespace (and not attached): > [1] RCurl_0.94-1 XML_2.3-0 > > > -- > Xiaoling > > _______________________________________________ > 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 >