Hi P.Terry, Thanks to both Wolfgang and Steffen for explaining the database situation! In stead of chasing down each duplicate entries in different databases, I decided to output one entry for each exon ID, and output a warning message alerting the users the list of exon ids with duplicated entries. This way the users who are the expert of the queried database, can choose to resolve the duplicated entries with the list of ids.
The fix is in dev 1.3.11. Best regards, Julie ******************************************* Lihua Julie Zhu, Ph.D Research Associate Professor Program Gene Function and Expression University of Massachusetts Medical School 364 Plantation Street, Room 613 Worcester, MA 01605 508-856-5256 http://www.umassmed.edu/pgfe/faculty/zhu.cfm ******************************************* On 3/5/10 6:46 PM, "[email protected]" <[email protected]> wrote: Dear bioc-sig-sequencing, I would like to annotate chip-seq peaks for the arabidopsis genome. "TSS" and "Exon" are two of the arguments for the 'getAnnotation' function. The "TSS" argument succeeded, but the "Exon" argument failed. ... > arabdset<-useMart(biomart="plant_mart_4", dataset = "athaliana_eg_gene") Checking attributes ... ok Checking filters ... ok > ExonArabAnno<-getAnnotation(arabdset, featureType="Exon") Error in `rownames<-`(`*tmp*`, value = c("ATCG00010.1-E176369", "ATMG00010.1-E176520", : duplicate rownames not allowed > sessionInfo() R version 2.11.0 Under development (unstable) (2010-02-28 r51186) x86_64-unknown-linux-gnu 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] ChIPpeakAnno_1.3.4 org.Hs.eg.db_2.3.6 [3] GO.db_2.3.5 RSQLite_0.8-3 [5] DBI_0.2-5 AnnotationDbi_1.9.4 [7] BSgenome.Ecoli.NCBI.20080805_1.3.16 BSgenome_1.15.11 [9] Biostrings_2.15.22 IRanges_1.5.51 [11] multtest_2.3.0 Biobase_2.7.4 [13] biomaRt_2.3.4 loaded via a namespace (and not attached): [1] MASS_7.3-5 RCurl_1.3-1 splines_2.11.0 survival_2.35-8 [5] tools_2.11.0 XML_2.6-0 > Can someone comment? Thanks, P. Terry [email protected] [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
