Hi @EmWhat
This error comes up when the tool cannot build a data structure properly during processing. This is an R error, so R formatting requirements need to be met.
The tool form has examples/detailed help for each of these:
- At least two groups are input
- Each group contains at least two count inputs
- The same number of count files were input per group
- Labels for groups are all “oneword” or “one_word”. Alphanumeric characters plus (optionally) underscores.
- If you are inputting a matrix instead of individual count files, the same labeling rules would apply.
- Same for contrast inputs – full group labels separated by a dash “-”.
- Whitespace or any other characters will cause interpretation problems.
If you can’t find the problem, please post back either a shared history link or a screenshot of the job details page for one of the errored outputs (specifically, the portion of the log where the tool version and inputs/parameters are listed out). How to do both is explained here troubleshooting-errors
Let’s start there 
Related prior Q&A: edgeR error in galaxy