ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays

Motivation: Current algorithms for estimating DNA copy numbers (CNs) borrow concepts from gene expression analysis methods. However, single nucleotide polymorphism (SNP) arrays have special characteristics that, if taken into account, can improve the overall performance. For example, cross hybridization between alleles occurs in SNP probe pairs

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ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays

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