Hey, everybody, tonight is a wonderful time to start my journey on your resource. Although, it was not much anticipated before today, I had performed some brief ontology enrichment analyses on the data from publicly available microarray runs. Pretty skeptical about this, but having my RNA sequencing results output from DeSEQ2 and eager to generate some figures for my boss, for us to see what is going on. I try to run the following command, only for it to tell me that the input does not match the required format, when I clearly see that it is not true. Therefore, I am using Biostars and I am pleased to announce that I will be using this forum, since I am getting back in touch for some experiments with my lab. Please if anybody knows how to fix this bug, I would kindly appreciate your contribution in comment section. Otherwise, lets just all be patient and a drunk beer god be kind and generous and continue to cast some bioinformatics upon us.
GO.params.bp <- GSEAGOHyperGParams(name="GOstats",
geneSetCollection=gene_annotations,
geneIds = ensembl_gene_ids,
universeGeneIds = NULL,
ontology = "BP",
pvalueCutoff = cutoff,
conditional = FALSE,
testDirection = "over")
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘geneIdType’ for signature ‘"character"’
str(ensembl_gene_ids)
chr [1:3] "ENSG00000100592" "ENSG00000101336" "ENSG00000134285"
class(ensembl_gene_ids)
[1] "character"
