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How can the Mismatch probe cell have a higher intensity than its complementary Perfect Match probe cell?
There can be a number of reasons for this, including:
  • It is possible that the probe sequence has high homology with another unknown sequence, resulting in a high Mismatch-to-Perfect Match ratio.
  • Another possibility is that the probe sequence on the array is correct for the majority of the cases, however, the sample may have a sequence variation that causes low specific binding to the Perfect Match, and high specific binding to the Mismatch.

Regardless of the cause, the redundancy of the number of probes representing a sequence on GeneChip® expression arrays negates any significant impact this may have on the final interpretation of the data.