Dear all, I am trying to use the biomaRt package to retrieve data from the Ensembl database. However, I get an error message using the useDataset() function. I think this is perhaps because useDataset() does not expect Ensembl datasets to have spaces in their names, but some do. I have typed the following to try to select the Mycobacterium ulcerans dataset from the Ensembl Bacteria database: library("biomaRt") ensemblbacteria <- useMart("bacterial_mart_9") listDatasets(ensemblbacteria) This tells me that the name of the Mycobacterium ulcerans data set is "EB 1 m_ulcerans". However, when I try to select it using useDataset() I get an error message: ensemblMulcerans <- useDataset("EB 1 m_ulcerans",mart=ensemblbacteria) Error in useDataset("EB 1 m_ulcerans", mart = ensemblbacteria) : The given dataset: EB 1 m_ulcerans , is not valid. Correct dataset names can be obtained with the listDatasets function. I think this could be because useDataset does not expect dataset names to contain spaces? I would be grateful for any help with this. Kind Regards, Avril Avril Coghlan Cork, Ireland

Hi Avril "EB 1 m_ulcerans" looks like the 'version' of the dataset to me. check: > listDatasets(ensemblbacteria)[82,] dataset description 82 myc_25870_gene Mycobacterium ulcerans genes (EB 1 m_ulcerans) version 82 EB 1 m_ulcerans > Hence, if I do: > ensemblMulcerans <- useDataset("myc_25870_gene",mart=ensemblbacteria) > I can do stuff like: > getBM(attributes=c("ensembl_transcript_id", "transcript_start"), filters=c("chromosome_name", "start","end"), values=list("pMUM001", "1", "10000"),ensemblMulcerans) ensembl_transcript_id transcript_start 1 EBMYCT00000077424 6612 2 EBMYCT00000077394 1694 3 EBMYCT00000077445 7630 4 EBMYCT00000077427 6383 5 EBMYCT00000077446 8430 6 EBMYCT00000077396 2921 7 EBMYCT00000077437 7188 8 EBMYCT00000077402 5640 9 EBMYCT00000077412 1 10 EBMYCT00000077408 2310 11 EBMYCT00000077390 1117 > I hope this helps Regards, Hans > sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.8.0 loaded via a namespace (and not attached): [1] RCurl_1.5-0 XML_3.2-0 > On 06/24/2011 06:05 PM, Coghlan, Avril wrote: > Dear all, > > I am trying to use the biomaRt package to retrieve data from the Ensembl > database. > However, I get an error message using the useDataset() function. > I think this is perhaps because useDataset() does not expect Ensembl > datasets to have spaces in their names, but some do. > > I have typed the following to try to select the Mycobacterium ulcerans > dataset from the Ensembl Bacteria database: > library("biomaRt") > ensemblbacteria<- useMart("bacterial_mart_9") > listDatasets(ensemblbacteria) > This tells me that the name of the Mycobacterium ulcerans data set is > "EB 1 m_ulcerans". > > However, when I try to select it using useDataset() I get an error > message: > ensemblMulcerans<- useDataset("EB 1 > m_ulcerans",mart=ensemblbacteria) > > Error in useDataset("EB 1 m_ulcerans", mart = ensemblbacteria) : > The given dataset: EB 1 m_ulcerans , is not valid. Correct dataset > names can be obtained with the listDatasets function. > > I think this could be because useDataset does not expect dataset names > to contain spaces? > > > I would be grateful for any help with this. > > Kind Regards, > Avril > > Avril Coghlan > Cork, Ireland > > _______________________________________________ > 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