Model-based analysis of two-color arrays (MA2C)

A novel normalization method based on the GC content of probes is developed for two-color tiling arrays. The proposed method, together with robust estimates of the model parameters, is shown to perform superbly on published data sets. A robust algorithm for detecting peak regions is also formulated...

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Detalles Bibliográficos
Autores principales: Song, Jun S, Johnson, W Evan, Zhu, Xiaopeng, Zhang, Xinmin, Li, Wei, Manrai, Arjun K, Liu, Jun S, Chen, Runsheng, Liu, X Shirley
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375008/
https://www.ncbi.nlm.nih.gov/pubmed/17727723
http://dx.doi.org/10.1186/gb-2007-8-8-r178
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author Song, Jun S
Johnson, W Evan
Zhu, Xiaopeng
Zhang, Xinmin
Li, Wei
Manrai, Arjun K
Liu, Jun S
Chen, Runsheng
Liu, X Shirley
author_facet Song, Jun S
Johnson, W Evan
Zhu, Xiaopeng
Zhang, Xinmin
Li, Wei
Manrai, Arjun K
Liu, Jun S
Chen, Runsheng
Liu, X Shirley
author_sort Song, Jun S
collection PubMed
description A novel normalization method based on the GC content of probes is developed for two-color tiling arrays. The proposed method, together with robust estimates of the model parameters, is shown to perform superbly on published data sets. A robust algorithm for detecting peak regions is also formulated and shown to perform well compared to other approaches. The tools have been implemented as a stand-alone Java program called MA2C, which can display various plots of statistical analysis for quality control.
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spelling pubmed-23750082008-05-12 Model-based analysis of two-color arrays (MA2C) Song, Jun S Johnson, W Evan Zhu, Xiaopeng Zhang, Xinmin Li, Wei Manrai, Arjun K Liu, Jun S Chen, Runsheng Liu, X Shirley Genome Biol Method A novel normalization method based on the GC content of probes is developed for two-color tiling arrays. The proposed method, together with robust estimates of the model parameters, is shown to perform superbly on published data sets. A robust algorithm for detecting peak regions is also formulated and shown to perform well compared to other approaches. The tools have been implemented as a stand-alone Java program called MA2C, which can display various plots of statistical analysis for quality control. BioMed Central 2007 2007-08-29 /pmc/articles/PMC2375008/ /pubmed/17727723 http://dx.doi.org/10.1186/gb-2007-8-8-r178 Text en Copyright © 2007 Song et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
Song, Jun S
Johnson, W Evan
Zhu, Xiaopeng
Zhang, Xinmin
Li, Wei
Manrai, Arjun K
Liu, Jun S
Chen, Runsheng
Liu, X Shirley
Model-based analysis of two-color arrays (MA2C)
title Model-based analysis of two-color arrays (MA2C)
title_full Model-based analysis of two-color arrays (MA2C)
title_fullStr Model-based analysis of two-color arrays (MA2C)
title_full_unstemmed Model-based analysis of two-color arrays (MA2C)
title_short Model-based analysis of two-color arrays (MA2C)
title_sort model-based analysis of two-color arrays (ma2c)
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375008/
https://www.ncbi.nlm.nih.gov/pubmed/17727723
http://dx.doi.org/10.1186/gb-2007-8-8-r178
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