Dear Adrian and all I am using the package topGO and I would like to know if you could help me to reuse the same object to perform several test, see the examples below:
library("topGO") data(GOdata) geneSelectionFun(GOdata) <- function(x) {x == 1L} GOdata resultKS.elim <- runTest(GOdata, algorithm = "elim", statistic = "ks") allRes1 <- GenTable(GOdata, resultKS.elim) geneSelectionFun(GOdata) <- function(x) {x > 0.5} GOdata resultKS.elim2 <- runTest(GOdata, algorithm = "elim", statistic = "ks") allRes2 <- GenTable(GOdata, resultKS.elim2) ontology(GOdata) <- "CC" resultKS.elim3 <- runTest(GOdata, algorithm = "elim", statistic = "ks") allRes3 <- GenTable(GOdata, resultKS.elim3) all.equal(score(resultKS.elim), score(resultKS.elim2)) # Shouldn't it be different? all(names(score(resultKS.elim3)) == names(score(resultKS.elim2))) # Should the GO terms be different? sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.2 LTS locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=es_ES.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=es_ES.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] topGO_2.26.0 SparseM_1.74 GO.db_3.4.0 [4] AnnotationDbi_1.36.2 IRanges_2.8.1 S4Vectors_0.12.1 [7] Biobase_2.34.0 graph_1.52.0 BiocGenerics_0.20.0 loaded via a namespace (and not attached): [1] Rcpp_0.12.9 matrixStats_0.51.0 lattice_0.20-34 digest_0.6.12 [5] grid_3.3.2 DBI_0.5-1 RSQLite_1.1-2 tools_3.3.2 [9] memoise_1.0.0 The object GOdata have different number of "Significant" genes annotated when I change the geneSelectionFun, thus I would expect different p-values but there are the same p-values in allRes2 and allRes1. Also the test on the cellular component returns the same genes ontologies as the previous test, which should be different because it is performed in a different GO subcategory. Maybe that's the reason why the Term column is NA. I am doing something wrong? How can I reuse the same object with different tests? Thanks your help Lluís [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel