Hello,

I used edger to detect differentially expressed genes based on my RNA-seq data from Rattus Norvegicus samples.

I obtained a list of DE genes and I used the 'kegga' function from the limma package in order to detect kegg pathways with abnormal number of DE genes.

In the result, I obtain a list of kegg pathway and the corresponding number of DE genes and associated p-values.

For some of these pathways (e.g. rno05166), I can not find the list of the genes that are implicated in this pathway so I can not find out if these genes tend to be up- or down- regulated.

library(Rattus.norvegicus)
ENTREZ <- keys(Rattus.norvegicus,keytype = 'ENTREZID')
annot.path <- select(Rattus.norvegicus,keytype = 'ENTREZID',keys=ENTREZ,columns = 'PATH')
select(Rattus.norvegicus,keytype = 'PATH',keys='03030',columns = 'ENTREZID')
select(Rattus.norvegicus,keytype = 'PATH',keys='05166',columns = 'ENTREZID')

For pathway '05166', the following error message is produced:

None of the keys entered are valid keys for 'PATH'. Please use the keys method to see a listing of valid arguments.

How to explain that the 'kegga' function found some genes in the pathway while this pathway is absent in the Rattus.norvegicus annotation package?

Many thanks

Jérôme