Hi @battagliad1
This error can also result from labels or data structures that the tool cannot interpret. It is a R tool that is very picky about format. The same error would result from using it line-command with the same inputs/parameters.
This is a good post about how to check the data, since it goes through a few tools, including this one, with common format troubleshooting: EdgeR row names error
Short list of things to check:
- No extra headers in either file. Remove if needed.
- Do the geneIDs have a
.N(where N is a version number) attached at the end? Try removing the.versionand confirm that all IDs are unique. - Are the geneIDs in the same order between the two inputs?
- Some people have had success with filtering down both files to contain the same genes (only).
- Technically, what is required is that each gene in the gene-true/false input is represented in the gene-lengths file (just one time, and that second gene-lengths file can have excess genes). But doing this can sometimes identify problems.
See Data Manipulation Olympics or that other topic above for how to do the data manipulations/comparisons.
Let’s start there, thanks! 