Still having problems with edgeR. I was able to get DeSeq2 to work by using very simple names for factor name and levels. This does not work for edgeR. I still get the following error
An error occurred with this dataset:
Fatal error: Exit code 1 ()
*tmp*, value = c("X0", "X0", "X0", :
duplicate 'row.names' are not allowed
Calls: row.names<- -> row.names<-.data.frame
non-unique value when setting 'row.names': ‘X0’
Seems like a data format error. Is it the header? Or is it some data line in the file that it doesn't like?
BTW: I greatly appreciate all your help in getting to this point in the analysis. Thank you for your quick responses and very helpful comments.