I am trying to run a gene ontology analysis but my reference species is A.thaliana available here: org.At.tair.db. However, the function goana doesn't recognize species "At" and performs the GO enrichment against the human genome.
Kegga seems to recognize species "At" but I get the following error:
Error in kegga.default(de = DEGenes, universe = universe, ...) : Pathways do not overlap with universe
Please any help is much appreciated.
It's actually Ath not At and there are more subspecies of Arabidopsis. See here all the 3 letter codes for plant species: https://www.kegg.jp/kegg-bin/show_organism?category=Eudicots
My answer was correct as written. Please read the ?kegga documentation.
keggaallows species names to be specified in either Bioconductor format (two letters) or KEGG format (three letters) via the two arguments
species.KEGG. Also, the KEGG species names are all lowercase so your
"Ath"is not correct.