> genesList <- degs$P.Value > names(genesList) <- degs$ENTREZID > sampleGOdata <- - new("topGOdata", + description = "Simple session", ontology = "BP", + allGenes = genesList, geneSel = function(x){x<0.01}, + nodeSize = 10, + annot = annFUN.org,mapping="org.Hs.eg.db", ID = "entrez") Building most specific GOs ..... ( 462 GO terms found. ) Build GO DAG topology .......... ( 2076 GO terms and 4544 relations. ) Annotating nodes ............... ( 66 genes annotated to the GO terms. ) Error in -new("topGOdata", description = "Simple session", ontology = "BP", : invalid argument to unary operator
I'm not sure what exactly is wrong, could be older version of the package, namely 1.0.2, while R is 3.4.4. But I don't want to update, because the pipeline is fixed. Any help is much appreciated. I tried to debug, but it's a bit obscure. Below is session information:
> sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.5 LTS Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=uk_UA.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=uk_UA.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=uk_UA.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=uk_UA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] org.Hs.eg.db_3.5.0 topGO_2.30.1 SparseM_1.77 GO.db_3.5.0 AnnotationDbi_1.40.0 [6] IRanges_2.12.0 S4Vectors_0.16.0 Biobase_2.38.0 graph_1.56.0 BiocGenerics_0.24.0 [11] GOplot_1.0.2 RColorBrewer_1.1-2 gridExtra_2.3 ggdendro_0.1-20 ggplot2_3.1.0 [16] enrichR_1.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.0 pillar_1.3.0 compiler_3.4.4 plyr_1.8.4 bindr_0.1.1 [6] tools_3.4.4 digest_0.6.18 bit_1.1-14 lattice_0.20-35 memoise_1.1.0 [11] RSQLite_2.1.1 tibble_1.4.2 gtable_0.2.0 pkgconfig_2.0.2 rlang_0.3.0.1 [16] DBI_1.0.0 rstudioapi_0.8 curl_3.2 bindrcpp_0.2.2 withr_2.1.2 [21] dplyr_0.7.8 httr_1.3.1 bit64_0.9-7 grid_3.4.4 tidyselect_0.2.5 [26] glue_1.3.0 R6_2.3.0 blob_1.1.1 purrr_0.2.5 magrittr_1.5 [31] matrixStats_0.54.0 scales_1.0.0 MASS_7.3-50 assertthat_0.2.0 colorspace_1.3-2 [36] lazyeval_0.2.1 munsell_0.5.0 crayon_1.3.4 rjson_0.2.20 |
|
|
You will most likely need to give more information than that. Unless someone (probably Adrian Alexa) can reproduce the error you are seeing, it's not usually possible to debug. If your
genesList
isn't too massive, you could probably just paste the output fromdput
. But more likely you need to save as an.Rdata
file and put somewhere (say DropBox) with a link so people can try to reproduce.I reduced the data file, will this do for the debugging? Also additional question, when I reduce the file even more (and obviously it cannot find any terms) it also gives an error: