[bigmw]

BTW, if the gene IDs look similar to the KEGG gene ID (locus tag), like "SPAC15A10.01" "SPBC25B2.02c" etc, you don’t need to convert the gene IDs. Because they are already the same as those used in the KEGG pathways or gene set data (kegg.gs). you can check the format of the gene ID of cufflinks output:
head(gnames)

I have one more question! In part 6.5 of "RNA-seqworkflow" working on cufflinks data. how should I change the ID conversion line? Should I leave it as it is or KEGG?

> gnames.eg=pathview::id2eg(gnames, category ="symbol")