Hi,
It is a bit challenging to give you a precise answer based on the limited information you provided but I wonder if your Samples variable is only represented in specific Batches, as shown below:
Batch 1 - Sample A
Batch 1 - Sample B
Batch 1 - Sample C
Batch 2 - Sample D
Batch 2 - Sample E
...
If it is the case, there is not information for JMP to test the effect across your variables. You may want to explore the functionality of Nesting Sample within Batch: Sample[Batch]?
Best,
TS
Thierry R. Sornasse