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Affymetrix® Genotyping Console™ Software
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QC for Copy Number Analysis
What are the passing thresholds in GTC 3.0.1 for the Median Absolute Pairwise Difference (MAPD) metric?
The MAPD passing thresholds for SNP Array 6.0 copy number data are as follows:
- Affymetrix Reference – passing MAPD is 0.35 or less (Derived from the HapMap 270 data set)
- External Reference – passing MAPD is 0.35 or less (Chips generated in different lab and with different reagent lots)
- Internal Reference – passing MAPD is 0.30 or less (Chips generated in same lab with same reagent lots)