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Typically, a negative Average Difference value means that, overall, the intensities of the Mismatch probe cells are higher than the corresponding Perfect Match probe cells. The Mismatch probe cells are designed to account for any cross-hybridization that may occur in the sample. The "real" intensity is calculated by subtracting the Mismatch intensity from the Perfect Match intensity. A strong hybridization signal at a Mismatch probe cell may, in rare cases, be associated with a polymorphism. However, the GeneChip® expression assay is not specifically designed to detect or discriminate polymorphisms.
A negative Average Difference value occurs, in three cases, when:
- The majority of the Mismatch probe cells are higher in intensity than the Perfect Match probe cells.
- A few of the Mismatch probe cells are significantly higher than the Perfect Match probe cells (and under the threshold for "superscoring"), skewing the Average Difference to a negative value.
- A limitation in the Microarray Suite software may cause a very-high negative Average Difference value. The software can only accept a certain number of digits in the Average Difference value field. If the size of this number exceeds the maximum number of digits allowed (usually caused by scaling/normalization), the last digit corresponds to a positive/negative sign. If many large negative Average Difference values are observed, re-analyze the data using a lower target intensity.
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