What does a negative Average Difference value mean?
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 Microarr
