I'm using edgeR
to perform a a RNA-seq differential expression analysis with S. cerevisiae samples and then trying to use goana
. My genes ids are from ensembl so I added a column with entrezgene ids to the DGELRT
object, which is coming from the glmQLFTest
function. I'm not sure where in the DGLRT object I have to add the column with entrezgene ids, in the manual says:
...or the name of the column of de$genes containing the Gene IDs.
But I cannot find which element in the DGELRT
object is de$genes
, so I added to de$table
and I'm passing that to goana
. I also tried to add the entregene ids to dgelist_qltest$geneid
but goana
fails in the same way
> class(dgelist_qltest)
[1] "DGELRT"
attr(,"package")
[1] "edgeR"
> goana.DGELRT(de=dgelist_qltest, geneid=dgelist_qltest$table$entrezgene_id)
Error in goana.default(de = DEGenes, universe = universe, ...) :
No annotated genes found in universe
> head(dgelist_qltest$table)
logFC logCPM F PValue entrezgene_id
YAL001C 0.2240038 6.943048 14.1162483 0.0022238429 851262
YAL002W 0.2994297 6.364025 18.9983099 0.0006987048 851261
YAL003W -0.3346512 10.272637 10.8792050 0.0054613104 851260
YAL004W 0.1465868 7.660092 0.8873887 0.3657633848 NA
YAL005C 0.2767830 11.574323 4.7249463 0.0479133341 851259
YAL007C -0.2657464 7.172642 8.8780937 0.0102093078 851226
#When I pass this to goana, fails with the same error:
> head(dgelist_qltest$geneid)
[1] 851262 851261 851260 NA 851259 851226
Related to this, when I use goana
with (or without) the geneid
parameter and species=...
I get this error:
> goana(de=dgelist_qltest, geneid=dgelist_qltest$table$entrezgene_id, species='Sc')
Error in goana.default(de = DEGenes, universe = universe, ...) :
org.Sc.eg.db package required but not not installed (or can't be loaded)
Where the name of the db isn't found because in the case of S. cerevisiae is org.Sc.sgd.db
, which does have "sgd" instead of the "eg" in the name.

