Hi Ligang, A week ago or so there was a new release of Ensembl (This usually happens every two months). Normally there are few changes in attribute names, however there were some attribute name changes in this release. Use the command below to get all attributes related to structures. You'll see that you now have to use ensembl_exon_id, rank, exon_chrom_end and exon_chrom_start do get what you want. Cheers, Steffen > listAttributes(mart,category="Structures") name 1 ensembl_exon_id 2 exon_chrom_end 3 exon_chrom_start 4 phase 5 rank 6 struct_transcript_count 7 structure_biotype 8 structure_canonical_transcript_id 9 structure_cdna_length 10 structure_cds_length 11 structure_chrom_name 12 structure_description 13 structure_external_db_name 14 structure_external_gene_id 15 structure_gene_chrom_end 16 structure_gene_chrom_start 17 structure_gene_stable_id 18 structure_peptide_length 19 structure_transcript_chrom_end 20 structure_transcript_chrom_start 21 structure_transcript_chrom_strand 22 structure_transcript_stable_id 23 structure_translation_stable_id description 1 Ensembl Exon ID 2 Exon Chr End (bp) 3 Exon Chr Start (bp) 4 phase 5 Exon Rank in Transcript > hello, there, > > > I run into some problems in using biomaRt to mine the transcript > structures: > > ============== > library(biomaRt) > mart<-useMart("ensembl", dataset="hsapiens_gene_ensembl") > listAttributes(mart)$name->attrs > attrs[grep("exon",attrs)] > ============== > > > > why "structure_exon_stable_id", "structure_exon_chrom_start", > "structure_exon_chrom_end" and "structure_exon_rank" are not avaliable? > > > > ================ > sessionInfo() > R version 2.7.1 (2008-06-23) > 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] grid stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] GenomeGraphs_1.0.0 biomaRt_1.14.0 RCurl_0.9-4 > > loaded via a namespace (and not attached): > [1] tools_2.7.1 XML_1.96-0 > ================= > > > Thanks, > > --- > Ligang > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 >