Im a noob with a very unclear idea of what I am doing, but I'm doing my best.
The other day, the ncbi webpage for downloading genomes and GTF files was down. As a result, I had to do my analysis on this RNA seq data using the ensembl files, which messed everything I know how to do up, and now my GSEA is in the ensemble ID (ie ENSMUSG00000000001) instead of a nice, clean, and easy to read gene ID (ie Gnai3)
Below is what I used to generate the GSEA
gse <- gseGO(geneList=gene_list, ont ="ALL", keyType = "ENSEMBL", minGSSize = 3, scoreType = "pos", maxGSSize = 800, pvalueCutoff = 0.05, verbose = TRUE, OrgDb = "org.Mm.eg.db", pAdjustMethod = "none")
I did try substituting the gene ID with the symbol using the second answer here, but got the following error
ensembl.genes <- (gene_list) gene_list ENSMUSG00000026166 ENSMUSG00000027514 ENSMUSG00000026582 ENSMUSG00000024401 ENSMUSG00000018916 8.3426962 8.2544408 8.1768632 7.7641708 7.6248835 ENSMUSG00000078365 ENSMUSG00000040026 ENSMUSG00000058427 ENSMUSG00000107750 ENSMUSG00000028287 7.0340698 6.6905516 6.4591807 6.2520667 6.1017208 ENSMUSG00000029380 ENSMUSG00000063171 ENSMUSG00000050587 ENSMUSG00000118159 ENSMUSG00000071341 5.5614790 5.5298819 4.9374363 4.7380874 4.5747161 ... [ reached getOption("max.print") -- omitted 2013 entries ] geneIDs1 <- ensembldb::select(EnsDb.Mmusculus.v79, keys= ensembl.genes, keytype = "GENEID", columns = c("SYMBOL", "GENEID")) Error in .select(x = x, keys = keys, columns = columns, keytype = keytype, : Argument keys should be a character vector, an object extending AnnotationFilter, a filter expression or an AnnotationFilterList.