Hi, I'm running the enrichPathway function:

x<-enrichPathway(gene=df$name, organism = "fly", pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.2, universe, minGSSize = 10, maxGSSize = 500, readable = FALSE)

and I get the error:

universe is not in character and will be ignored...

How is the universe parameter set? My understanding is that I don't have to pass any arguments but it seems that the background genes are not in character format? How is this function accessing the background genes?

Posted on Biostars, too: https://www.biostars.org/p/434669/

[just doing this to connect up and help both communities]

Check that the universe you input are characters and not numerics. The entrez ID are numbers so R recognizes them as numerics, but this function needs them to be characters.