PAIR: paired allelic log-intensity-ratio-based normalization method for SNP-CGH arrays

• DOI: 10.1093/bioinformatics/bts683
• Publication Date: 2012-11-30T03:17:56Z
• Authors: Shengping Yang; Stanley Pounds; Kun Zhang; Zhide Fang
• Keywords: Normalization; SNP

Abstract Motivation: Normalization is critical in DNA copy number analysis. We propose a new method to correctly identify two-copy probes from the genome obtain representative references for normalization single nucleotide polymorphism arrays. The based on two-state Hidden Markov Model. Unlike most currently available methods literature, proposed does not need assume that percentage of state dominant genome, as long there do exist probes. Results: real data analysis and simulation study show algorithm successful (i) it performs well current (e.g. CGHnormaliter popLowess) samples with states outperforms these less states; (ii) can copy-neutral loss heterozygosity; (iii) efficient terms computational time used. Availability: R scripts are at http://publichealth.lsuhsc.edu/PAIR.html. Contact: [e-mail] Supplementary information: Bioinformatics online.