The analysis of biases of copy numbers from affymetrix snp arrays

Affymetrix SNP arrays are widely used for both genome-wide association and copy number variation (CNV) studies, both of which depend on accurate copy number estimation. However, depending on the method used to copy number estimation, distortions from the actual copy numbers can occur. Therefore, we demonstrate here several effects that can bias accurate copy number estimation, and we describe how some of these biases can be adjusted by existing methods, while others require further study.