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Affymetrix® Genotyping Console™ Software

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QC for Copy Number Analysis

What is the Median Absolute Pairwise Difference (MAPD) metric?

MAPD is the recommended method of assessing noise in SNP Array 6.0 copy number data. The log2 distance between neighbors is calculated for all pairs and then the median is taken. This represents the typical distance between marker pairs with respect to log2 ratios. The higher the MAPD, the greater the noise between the array of interest and the reference set. MAPD values have a high correlation with IQR values.