Hello, Here is a problem with idMapper wrappers in AnnotationDbi. If you try to map in id that is not in the data base, the function breaks instead of returning a flag that allows handling the situation. >idConverter("NR_003620", srcSpecies="MUSMU", destSpecies="MUSMU", srcIDType="REFSEQ", destIDType="SYMBOL", keepMultGeneMatches=FALSE, keepMultProtMatches=FALSE, keepMultDestIDMatches = TRUE) Error in names(ans) <- unlist(make.name.tree(x, recursive, what.names), : attempt to set an attribute on NULL > sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] ggplot2_0.9.0 RSvgDevice_0.6.4.1 Vennerable_2.1 [4] xtable_1.7-0 reshape_0.8.4 plyr_1.7.1 [7] lattice_0.20-0 RBGL_1.30.1 graph_1.32.0 [10] venneuler_1.1-0 rJava_0.9-3 pheatmap_0.6.0 [13] heatmap.plus_1.3 RColorBrewer_1.0-5 Heatplus_2.1.0 [16] gplots_2.10.1 KernSmooth_2.23-7 caTools_1.12 [19] bitops_1.0-4.1 gdata_2.8.2 gtools_2.6.2 [22] org.Mm.eg.db_2.6.4 RSQLite_0.11.1 DBI_0.2-5 [25] AnnotationDbi_1.16.9 Biobase_2.14.0 rj_1.0.3-7 loaded via a namespace (and not attached): [1] IRanges_1.12.4 MASS_7.3-17 colorspace_1.1-1 dichromat_1.2-4 [5] digest_0.5.1 memoise_0.1 munsell_0.3 proto_0.3-9.2 [9] reshape2_1.2.1 rj.gd_1.0.3-3 scales_0.2.0 stringr_0.6 [13] tools_2.14.1 Thanks, Robert

Hi Robert, This method needs to be overhauled and updated now that we have made some other improvements to our infrastructure. A bug has been added to my issue tracker for future development and also: thanks for reporting this. It's also good to know that people are using this function. I was actually wondering if maybe I should deprecate it, but now I think that maybe I should update it instead. In the meantime I think you can get much the same functionality by using the new select methods. There is now even a select method for inparanoid in the latest development version of AnnotationDbi. The select methods handle missing IDs much more gracefully than the much older idConverter function, and they also allow you to recover multiple things at once. In the case you listed below you can already do this by using select like so; library(org.Mm.eg.db) keys = c("NR_003620","NM_007376") cols= c("SYMBOL","GENENAME") ## can add however many things you want here. keytype="REFSEQ" select(org.Mm.eg.db,keys=keys, cols=cols, keytype=keytype) Marc On 04/16/2012 10:21 AM, Faryabi, Robert (NIH/NCI) [F] wrote: > Hello, > > Here is a problem with idMapper wrappers in AnnotationDbi. > If you try to map in id that is not in the data base, the function breaks instead of returning a flag that allows handling the situation. > >> idConverter("NR_003620", srcSpecies="MUSMU", destSpecies="MUSMU", srcIDType="REFSEQ", destIDType="SYMBOL", keepMultGeneMatches=FALSE, keepMultProtMatches=FALSE, keepMultDestIDMatches = TRUE) > Error in names(ans)<- unlist(make.name.tree(x, recursive, what.names), : > attempt to set an attribute on NULL > > >> sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] ggplot2_0.9.0 RSvgDevice_0.6.4.1 Vennerable_2.1 > [4] xtable_1.7-0 reshape_0.8.4 plyr_1.7.1 > [7] lattice_0.20-0 RBGL_1.30.1 graph_1.32.0 > [10] venneuler_1.1-0 rJava_0.9-3 pheatmap_0.6.0 > [13] heatmap.plus_1.3 RColorBrewer_1.0-5 Heatplus_2.1.0 > [16] gplots_2.10.1 KernSmooth_2.23-7 caTools_1.12 > [19] bitops_1.0-4.1 gdata_2.8.2 gtools_2.6.2 > [22] org.Mm.eg.db_2.6.4 RSQLite_0.11.1 DBI_0.2-5 > [25] AnnotationDbi_1.16.9 Biobase_2.14.0 rj_1.0.3-7 > > loaded via a namespace (and not attached): > [1] IRanges_1.12.4 MASS_7.3-17 colorspace_1.1-1 dichromat_1.2-4 > [5] digest_0.5.1 memoise_0.1 munsell_0.3 proto_0.3-9.2 > [9] reshape2_1.2.1 rj.gd_1.0.3-3 scales_0.2.0 stringr_0.6 > [13] tools_2.14.1 > > Thanks, > Robert > > _______________________________________________ > 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.info rmatics.conductor