Hi, I have used org.Hs.egGO for mapping entrez ID in human to GO term successfully. However the mapping is not available in org.Sc.sgGO. So I tried to convert gene name to orf using org.Sc.sgdCOMMON2ORF mapping. Then I encountered the following error.
gene2orf = org.Sc.sgdCOMMON2ORF mapped_gene <- mappedkeys(gene2orf) xx <- as.list(gene2orf[mapped_genes]) Error in .checkKeys(value, Lkeys(x), x...@ifnotfound) : value for "15S_rRNA" not found Error in as.list(gene2orf[mapped_genes]) : error in evaluating the argument 'x' in selecting a method for function 'as.list The session information is the same as the following post. Thank you so much for your help! Best regards, Julie On 3/23/10 9:43 AM, "Zhu, Julie" <[email protected]> wrote: Hi, I have used org.Hs.egENSEMBL2EG in org.Hs.eg.db for mapping emsembl gene ID to entrez ID successfully. However it does not work for org.Sc.sgd.db. I tried to use org.Sc.sgdENSEMBL instead but got the ensembl ID back as mapping. Here is the code snippet to show the problem and session info. orgAnn <- get(paste("org.Sc.sgd", "ENSEMBL", sep = "")) OrgAnn IDs = c("YHR055C") xx[names(xx)==IDs[1]] ###### output the ensembl id instead of entrez id ####### $YHR055C [1] "YHR053C" "YHR055C" # sessionInfo() R version 2.10.0 (2009-10-26) i386-apple-darwin8.11.1 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] org.Sc.sgd.db_2.3.5 ChIPpeakAnno_1.3.15 limma_2.19.2 [4] org.Hs.eg.db_2.3.6 GO.db_2.3.5 RSQLite_0.7-1 [7] DBI_0.2-4 AnnotationDbi_1.8.1 BSgenome.Ecoli.NCBI.20080805_1.3.16 [10] BSgenome_1.14.2 Biostrings_2.14.8 IRanges_1.4.9 [13] multtest_2.1.2 Biobase_2.5.5 biomaRt_2.1.0 loaded via a namespace (and not attached): [1] MASS_7.3-3 RCurl_0.98-1 splines_2.10.0 survival_2.35-7 tools_2.10.0 XML_2.3-0 ENSEMBL map for Yeast (object of class "AnnDbBimap") Thank you very much for your help! Best regards, Julie ******************************************* Lihua Julie Zhu, Ph.D Research Associate Professor Program in 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 _______________________________________________ Bioconductor mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
