Start with the raw wells
Inspect the spatial pattern alongside the control distributions. Look for edge patterns, row or column shifts, and unusual individual wells. Compare the map with the dispensing layout, control positions, and reading order.
Use the pattern to choose a check
A pattern is a reason to investigate, not a diagnosis. Keep preparation and reader settings with the original data so you can compare runs without losing the context.
For the full discussion of misleadingly consistent controls, read A better Z′ can hide a worse measurement.