Dear Herve, Great. Thanks a lot for your work. Yours sincerely, Jianhong Ou LRB 670A Program in Gene Function and Expression 364 Plantation Street Worcester, MA 01605 On 11/16/13 6:51 AM, "Hervé Pagès" <hpages at="" fhcrc.org=""> wrote: >Hi Jianhong, > >Thanks for the report. Problem came from the fact that >makeTranscriptDbFromUCSC() was assuming that the "knownGene" table >was always associated with the "UCSC Genes" track but this appears to >not be true for old Human/Mouse/Rat assemblies where the track is >called "Known Genes". > >This is fixed in GenomicFeatures 1.14.1 (release) and 1.15.3 >(devel). Both should become available via biocLite() in the >next 30 hours or so. > >Cheers, >H. > > >On 11/13/2013 01:46 PM, Ou, Jianhong wrote: >> Hi, >> >> I got error when I make transcript db from ucsc for mm8. Could anybody >>help me to figure out this? Thanks in advance. >> >> Error in tableNames(ucscTableQuery(session, track = track)) : >> error in evaluating the argument 'object' in selecting a method for >>function 'tableNames': Error in normArgTrack(track, trackids) : Unknown >>track: UCSC Genes >> >> The codes: >> Library(GenomicFeatures) >> mm8KG <- makeTranscriptDbFromUCSC(genome="mm8", tablename="knownGene") >> >> 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 stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] GenomicFeatures_1.14.0 AnnotationDbi_1.24.0 Biobase_2.22.0 >> rtracklayer_1.22.0 GenomicRanges_1.14.3 XVector_0.2.0 >>IRanges_1.20.5 >> [8] BiocGenerics_0.8.0 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.18.0 Biostrings_2.30.0 bitops_1.0-6 >>BSgenome_1.30.0 DBI_0.2-7 RCurl_1.95-4.1 Rsamtools_1.14.1 >>RSQLite_0.11.4 stats4_3.0.2 >> [10] tools_3.0.2 XML_3.95-0.2 zlibbioc_1.8.0 >> >> Yours sincerely, >> >> Jianhong Ou >> >> LRB 670A >> Program in Gene Function and Expression >> 364 Plantation Street Worcester, >> MA 01605 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> > >-- >Hervé Pagès > >Program in Computational Biology >Division of Public Health Sciences >Fred Hutchinson Cancer Research Center >1100 Fairview Ave. N, M1-B514 >P.O. Box 19024 >Seattle, WA 98109-1024 > >E-mail: hpages at fhcrc.org >Phone: (206) 667-5791 >Fax: (206) 667-1319