Thanks a lot. I got it. Yours sincerely, Jianhong Ou jianhong.ou at umassmed.edu On Oct 8, 2011, at 6:22 AM, Hans-Rudolf Hotz wrote: > Hi > > Are you interested in the GenBank accession (equal to EMBL accession) or > the RefSeq accession? > > In any case you should follow the suggestion from the error message and > look at 'listAttributes', and then you will find, among many others: > > > 42 embl EMBL (Genbank) ID > > 74 ox_refseq_mrna__dm_dbprimary_acc_1074 RefSeq mRNA > > > Hence: > >> library(biomaRt) >> ensembl = useMart("ensembl") >> ensembl = useDataset("mmusculus_gene_ensembl",mart=ensembl) >> getBM(attributes = "embl", filters = > "ensembl_transcript_id",values=c("ENSMUST00000099400"),mart=ensembl) > embl > 1 CH466529 > 2 BC129896 > 3 BC129897 > 4 AF039957 > 5 AB030729 >> >> getBM(attributes = "ox_refseq_mrna__dm_dbprimary_acc_1074", filters = > "ensembl_transcript_id",values=c("ENSMUST00000099400"),mart=ensembl) > ox_refseq_mrna__dm_dbprimary_acc_1074 > 1 NM_019943 >> > > > > Hope this helps. > > Regards, Hans > > > >> sessionInfo() > R version 2.13.1 (2011-07-08) > 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_2.8.1 > > loaded via a namespace (and not attached): > [1] RCurl_1.6-6 XML_3.4-0 >> > > > > > > > On 10/07/2011 07:22 PM, Ou, Jianhong wrote: >> dear list, >> >> I use biomaRt to get the genBank access id for some ensembl transcript ids. >> >> library(biomaRt) >> ensembl = useMart("ensembl") >> ensembl = useDataset("mmusculus_gene_ensembl",mart=ensembl) >> access<-getBM(attributes = "refseq_dna", filters = "ensembl_transcript_id",values=ensembl_t_ids,mart=ensembl) >> >> I got error, >> Error in getBM(attributes = "refseq_dna", filters = "ensembl_transcript_id", : >> Invalid attribute(s): refseq_dna >> Please use the function 'listAttributes' to get valid attribute names >> >> What attributes should I use to instead "refseq_dna"? >> >> Yours sincerely, >> >> Jianhong Ou >> >> jianhong.ou at umassmed.edu >> >> _______________________________________________ >> 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