Error in .rowNamesDF<-(x, value = value) :
missing values in ârow.namesâ are not allowed
Calls: row.names<- -> row.names<-.data.frame -> .rowNamesDF<-
I would suggest using the Entrez IDs directly from Featurecounts instead to ensure distinct geneIDs. Then, at the end, you can convert those IDs to Ensembl for other purposes you may have.
Follow the tutorial, it will help to avoid problems like this.