A novel stationary wavelet denoising algorithm for array-based DNA Copy Number data

Abstract: High-throughput array-based assays have recently been developed to detect DNA copy number (DCN) aberrations. The DCN data from these arrays is characterized by high level of noise and unequal spacing of the probes on the genome. However, previously proposed denoising methods for DCN data did not consider the physical distances of the probes and assumed uniform spacing. It can be shown that denoising methods assuming uniform spacing for DCN data can potentially give incorrect results. To address this issue, we developed a novel stationary wavelet denoising scheme based on interpolation for DCN data. Empirical results on synthetic data showed that our method outperformed the best previously proposed wavelet denoising method by 4.6% – 12.7% as measured in the root mean squared error. Experiments on a real data set also confirmed the applicability of our method to real DCN data.

• Type: Journal
• Year: 2007
• Where: IJBRA
• Authors: Yuhang Wang, Siling Wang
• Keywords: DCN Data, Denoising, IJBRA 2007, Wavelet Denoising Scheme