rSWTi: A robust stationary wavelet denoising method for array CGH data

Yuhang Wang, Siling Wang, Andrew R. Zinn

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)

Abstract

High-throughput comparative genomic hybridization arrays have recently been developed to detect DNA copy number (DCN) aberrations. The DCN data from these arrays is often very noisy and thus calls for appropriate denoising methods. It has been recognized that a) the physical distances between adjacent probes are not uniform and that b) there are often outliers in the data. Previously proposed denoising methods for DCN data did not consider these two issues at the same time. In this paper, we address the two issues simultaneously in a new wavelet denoising scheme, called rSWTi (robust Stationary Wavelet Transform based denoising with interpolation), which extends the traditional stationary wavelet denoising approach. Empirical results on synthetic data showed that our method outperformed other methods by large margins as measured in the root mean squared error.

Original languageEnglish (US)
Title of host publicationProceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
Pages1066-1070
Number of pages5
DOIs
StatePublished - 2007
Event7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE - Boston, MA, United States
Duration: Jan 14 2007Jan 17 2007

Other

Other7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
CountryUnited States
CityBoston, MA
Period1/14/071/17/07

Fingerprint

DNA
Aberrations
Wavelet Analysis
Wavelet transforms
Comparative Genomic Hybridization
Interpolation
Throughput

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Bioengineering

Cite this

Wang, Y., Wang, S., & Zinn, A. R. (2007). rSWTi: A robust stationary wavelet denoising method for array CGH data. In Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE (pp. 1066-1070). [4375690] https://doi.org/10.1109/BIBE.2007.4375690

rSWTi : A robust stationary wavelet denoising method for array CGH data. / Wang, Yuhang; Wang, Siling; Zinn, Andrew R.

Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE. 2007. p. 1066-1070 4375690.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Wang, Y, Wang, S & Zinn, AR 2007, rSWTi: A robust stationary wavelet denoising method for array CGH data. in Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE., 4375690, pp. 1066-1070, 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE, Boston, MA, United States, 1/14/07. https://doi.org/10.1109/BIBE.2007.4375690
Wang Y, Wang S, Zinn AR. rSWTi: A robust stationary wavelet denoising method for array CGH data. In Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE. 2007. p. 1066-1070. 4375690 https://doi.org/10.1109/BIBE.2007.4375690
Wang, Yuhang ; Wang, Siling ; Zinn, Andrew R. / rSWTi : A robust stationary wavelet denoising method for array CGH data. Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE. 2007. pp. 1066-1070
@inproceedings{23562e9662a04abfb094d686132f7c75,
title = "rSWTi: A robust stationary wavelet denoising method for array CGH data",
abstract = "High-throughput comparative genomic hybridization arrays have recently been developed to detect DNA copy number (DCN) aberrations. The DCN data from these arrays is often very noisy and thus calls for appropriate denoising methods. It has been recognized that a) the physical distances between adjacent probes are not uniform and that b) there are often outliers in the data. Previously proposed denoising methods for DCN data did not consider these two issues at the same time. In this paper, we address the two issues simultaneously in a new wavelet denoising scheme, called rSWTi (robust Stationary Wavelet Transform based denoising with interpolation), which extends the traditional stationary wavelet denoising approach. Empirical results on synthetic data showed that our method outperformed other methods by large margins as measured in the root mean squared error.",
author = "Yuhang Wang and Siling Wang and Zinn, {Andrew R.}",
year = "2007",
doi = "10.1109/BIBE.2007.4375690",
language = "English (US)",
isbn = "1424415098",
pages = "1066--1070",
booktitle = "Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE",

}

TY - GEN

T1 - rSWTi

T2 - A robust stationary wavelet denoising method for array CGH data

AU - Wang, Yuhang

AU - Wang, Siling

AU - Zinn, Andrew R.

PY - 2007

Y1 - 2007

N2 - High-throughput comparative genomic hybridization arrays have recently been developed to detect DNA copy number (DCN) aberrations. The DCN data from these arrays is often very noisy and thus calls for appropriate denoising methods. It has been recognized that a) the physical distances between adjacent probes are not uniform and that b) there are often outliers in the data. Previously proposed denoising methods for DCN data did not consider these two issues at the same time. In this paper, we address the two issues simultaneously in a new wavelet denoising scheme, called rSWTi (robust Stationary Wavelet Transform based denoising with interpolation), which extends the traditional stationary wavelet denoising approach. Empirical results on synthetic data showed that our method outperformed other methods by large margins as measured in the root mean squared error.

AB - High-throughput comparative genomic hybridization arrays have recently been developed to detect DNA copy number (DCN) aberrations. The DCN data from these arrays is often very noisy and thus calls for appropriate denoising methods. It has been recognized that a) the physical distances between adjacent probes are not uniform and that b) there are often outliers in the data. Previously proposed denoising methods for DCN data did not consider these two issues at the same time. In this paper, we address the two issues simultaneously in a new wavelet denoising scheme, called rSWTi (robust Stationary Wavelet Transform based denoising with interpolation), which extends the traditional stationary wavelet denoising approach. Empirical results on synthetic data showed that our method outperformed other methods by large margins as measured in the root mean squared error.

UR - http://www.scopus.com/inward/record.url?scp=47649129281&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=47649129281&partnerID=8YFLogxK

U2 - 10.1109/BIBE.2007.4375690

DO - 10.1109/BIBE.2007.4375690

M3 - Conference contribution

AN - SCOPUS:47649129281

SN - 1424415098

SN - 9781424415090

SP - 1066

EP - 1070

BT - Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

ER -