Dear all,
I am trying to do a GO-term enrichment analysis in Drosophila ananassae with TopGO. I used the following code:
> sessionInfo() R version 3.3.0 (2016-05-03) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.4 LTS locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_DE.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] MeSH.Dan.eg.db_1.6.0 MeSHDbi_1.8.0 BiocInstaller_1.22.3 topGO_2.24.0 [5] SparseM_1.7 GO.db_3.3.0 AnnotationDbi_1.34.3 graph_1.50.0 [9] RColorBrewer_1.1-2 ggplot2_2.1.0 DESeq2_1.12.3 SummarizedExperiment_1.2.3 [13] Biobase_2.32.0 GenomicRanges_1.24.2 GenomeInfoDb_1.8.1 IRanges_2.6.1 [17] S4Vectors_0.10.1 BiocGenerics_0.18.0 loaded via a namespace (and not attached): [1] Rcpp_0.12.5 plyr_1.8.4 XVector_0.12.0 tools_3.3.0 zlibbioc_1.18.0 digest_0.6.9 [7] rpart_4.1-10 RSQLite_1.0.0 annotate_1.50.0 gtable_0.2.0 lattice_0.20-33 Matrix_1.2-6 [13] DBI_0.4-1 gridExtra_2.2.1 genefilter_1.54.2 cluster_2.0.4 locfit_1.5-9.1 grid_3.3.0 [19] nnet_7.3-12 data.table_1.9.6 XML_3.98-1.4 survival_2.39-5 BiocParallel_1.6.2 foreign_0.8-66 [25] latticeExtra_0.6-28 Formula_1.2-1 geneplotter_1.50.0 matrixStats_0.50.2 Hmisc_3.17-4 scales_0.4.0 [31] splines_3.3.0 colorspace_1.2-6 xtable_1.8-2 labeling_0.3 acepack_1.3-3.3 munsell_0.4.3 [37] chron_2.3-47
mytopgoobject <- new("topGOdata", description = "Slow15down", ontology = "BP", allGenes=Slow15downList, geneSel=topDiffGenes, annot=annFUN.org, nodeSize=5, mapping= "MeSH.Dan.eg.db")
and I get the following error message:
Building most specific GOs ..... Error in get(paste(mapping, "dbconn", sep = "_")) : object 'MeSH.Dan.eg_dbconn' not found
To me it seems like the annotation file for D. ananassae is not recognized. Can somebody help me and tell what I am doing wrong?
Thank you!!!!!!!!!!!!!!1