How can the mismatch probe cell have a higher intensity than its corresponding perfect match probe cell?
There could be a number of reasons for this. It is possible that this probe sequence has high homology with another unknown sequence resulting in a high mismatch-to-perfect match ratio. Another possibility is a mutation or set of mutations in the sequence of the target transcript which causes specific binding to the Mismatch. Regardless of the cause, the built-in redundancy using multiple probe pairs to represent a single sequence on the probe array mitigates any significant impact on the final interpretation of the data.