Entering edit mode
4.0 years ago
giulia.zancolli
•
0
Hello, I want to run gene set enrichment analysis based on gene expression values in TopGO but I cannot find an example in the TopGO tutorial nor in the manual. It does not say how the expression matrix should look like. I tried to create a TopGOdata object like this:
geneList = dat$TPM
names(geneList) = dat$gene
topDiffGenes = function(allScore) {return(allScore > 1)}
matrix = as.matrix(column_to_rownames(dat, "gene")) # convert the dataframe to matrix
GOdata = new("topGOdata", ontology = "BP", allGenes = geneList,
geneSel = topDiffGenes, annot = annFUN.gene2GO, gene2GO = bpGO, nodeSize = 5,
expressionMatrix = matrix)
And then I run the test:
runTest(GOdata, algorithm = "elim", statistic = "globaltest")
But I get the error:
Error in getSigGroups(object, test.stat) : No expression data found
How can I correctly load the expression matrix in the TopGOdata object?
Here the sessionInfo:
sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] tibble_3.0.0 topGO_2.38.1 SparseM_1.78 GO.db_3.10.0 AnnotationDbi_1.48.0 IRanges_2.20.2
[7] S4Vectors_0.24.3 Biobase_2.46.0 graph_1.64.0 BiocGenerics_0.32.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4 rstudioapi_0.11 magrittr_1.5 bit_1.1-15.2 lattice_0.20-41 rlang_0.4.5 fansi_0.4.1
[8] blob_1.2.1 tools_3.6.2 grid_3.6.2 cli_2.0.2 DBI_1.1.0 ellipsis_0.3.0 matrixStats_0.56.0
[15] assertthat_0.2.1 yaml_2.2.1 bit64_0.9-7 digest_0.6.25 lifecycle_0.2.0 crayon_1.3.4 vctrs_0.2.4
[22] glue_1.4.0 memoise_1.1.0 RSQLite_2.2.0 pillar_1.4.3 compiler_3.6.2 pkgconfig_2.0.3
Thank you!
Giulia