Seems I have found the problem. Despite Galaxy saying “NOTE: Please only use letters, numbers or underscores” when inputing factors manually, it seems you can’t use numbers for Groups when you use a factor file instead of manual input.
Indeed, when I changed my file to the following, it worked. I added an X in front of the Patient numbers.
| Sample | Tissue | Patient |
|---|---|---|
| M1 | M | X1 |
| M4 | M | X4 |
| M7 | M | X7 |
| M10 | M | X10 |
| M13 | M | X13 |
| N1 | N | X1 |
| N4 | N | X4 |
| N7 | N | X7 |
| N10 | N | X10 |
| N13 | N | X13 |