Hi Everyone

I am new to using gage and pathway view to get some view about my genes. My edgeR genes are using symbols like this: INSM1, LTF, JAK2, ..etc. I tried to change the DB to EnsDb but still doesn't work with me. I don't think the figures generated are for the genes I have as it seems they fail to be mapped to pathway. Any help please? Thanks

#edgeR code here 
#in summary the final two steps are: 
et <- exactTest(dge, pair=c("Control", "treated"))
etp <- topTags(et, n= 100000)
#Gage and pathview 
kegg.sets.hs = kegg.sets.hs[sigmet.idx.hs]
head(kegg.sets.hs, 3)
res = etp$table
foldchanges = res$logFC
names(foldchanges) = res$symbol
keggres = gage(foldchanges, gsets=kegg.sets.hs, same.dir=TRUE)
lapply(keggres, head)
keggrespathways = data.frame(id=rownames(keggres$greater), keggres$greater) %>%
  tbl_df() %>%
  filter(row_number()<=10) %>%
  .$id %>%
  as.character()
keggrespathways
keggresids = substr(keggrespathways, start=1, stop=8)
keggresids
data(go.sets.hs)
data(go.subs.hs)
gobpsets = go.sets.hs[go.subs.hs$BP]
gobpres = gage(foldchanges, gsets=gobpsets, same.dir=TRUE)
lapply(gobpres, head)

# Define plotting function for applying later
plot_pathway = function(pid) pathview(gene.data=foldchanges,gene.idtype="SYMBOL", pathway.id=pid, species="hsa")
# plot multiple pathways (plots saved to disk and returns a throwaway list object)
tmp = sapply(keggresids, function(pid) pathview(gene.data=foldchanges,gene.idtype="SYMBOL", pathway.id=pid, species="hsa"))

These are the warnings and the generated pathway figures don't include any of my interesting genes.

Warning: None of the genes or compounds mapped to the pathway! Argument gene.idtype or cpd.idtype may be wrong.

select()' returned 1:1 mapping between keys and columns Info: Working in directory Info: Writing image fil hsa00232.pathview.png Warning: None of the genes or compounds mapped to the pathway! Argument gene.idtype or cpd.idtype may be wrong.

'select()' returned 1:1 mapping between keys and columns Info: Working in directory Info: Writing image file hsa00983.pathview.png Warning: None of the genes or compounds mapped to the pathway! Argument gene.idtype or cpd.idtype may be wrong.

'select()' returned 1:1 mapping between keys and columns Info: Working in directory /.. Info: Writing image file hsa00230.pathview.png Warning: None of the genes or compounds mapped to the pathway! Argument gene.idtype or cpd.idtype may be wrong.

'select()' returned 1:1 mapping between keys and columns Info: Working in directory Info: Writing image file hsa04514.pathview.png Warning: None of the genes or compounds mapped to the pathway! Argument gene.idtype or cpd.idtype may be wrong.

'select()' returned 1:1 mapping between keys and columns Info: Working in directory Info: Writing image file hsa04010.pathview.png There were 50 or more warnings (use warnings() to see the first 50)