I am trying to analyze the DE genes from rna-seq data, but when I try to use the goana function I get the error message "No annotated genes found in universe". I believe this is because the genes are annotated with the gene IDs from Ensembl instead of the ones from RefSeq. Nevertheless, I can still perform GO analyses with Ensembl ID with a different program, but I need a list of the DE genes so I can select them to proceed with the GO analyses. How can I get a list of the up and down regulated genes from the edgeR?

Best regards, Rodrigo.

See ?topTags

If you are interested in all the up- and down-regulated DE genes at an FDR cut-off of 0.05, you can try

out <- topTags(object, n = Inf, p = 0.05)$table
DE.up <- out[out$logFC>0, ]
DE.down <- out[out$logFC<0, ]

you can use 'FDR' and 'logFC' columns in the output of the function topTags