After completing my annotation of non-model organism with GO terms and conducting GSEA etc I wanted to compare the most differentially expressed GO terms across the three used species with the goProfiles package (Bioconductor).
I tried creating the basicProfiles with this code, which worked but deliverd zero frequencies:
Cagla <- read.csv("CG_geneid_goid_test1.csv", header = T, sep="\t")
Cafin.MF <- basicProfile(Cafin, idType = "GOTermsFrame", onto="MF", level=2)
The initial Cafin data frame looks like this:
GeneID Ontology Evidence GOID
1 110826457 MF IEA GO:0004888
But even if I calculated the frequencies (occurrence of GO term in data frame Cafin) manually, creating the mergedProfileList results in the error:
allcalanus.MF <-mergeProfilesLists(Cafin.MF, Cahyp.MF, Cagla.MF, profNames=c("Cafin", "Cahyp", "Cagla"))
Error in !emptyCats : invalid argument type
Can anybody help me?