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A Bayes Regression Approach to Array-CGH Data

  • Chi-Chung Wen , Yuh-Jenn Wu , Yung-Hsiang Huang , Wei-Chen Chen , Shu-Chen Liu , Shih Sheng Jiang , Jyh-Lyh Juang , Chung-Yen Lin , Wen-Tsen Fang , Chao Agnes Hsiung und I-Shou Chang
Veröffentlicht/Copyright: 16. Februar 2006
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Statistical Applications in Genetics and Molecular Biology
Aus der Zeitschrift Statistical Applications in Genetics and Molecular Biology Band 5 Heft 1

This paper develops a Bayes regression model having change points for the analysis of array-CGH data by utilizing not only the underlying spatial structure of the genomic alterations but also the observation that the noise associated with the ratio of the fluorescence intensities is bigger when the intensities get smaller. We show that this Bayes regression approach is particularly suitable for the analysis of cDNA microarray-CGH data, which are generally noisier than those using genomic clones. A simulation study and a real data analysis are included to illustrate this approach.

Keywords: change point problem; comparative genomic hybridization; DNA copy number imbalance
Published Online: 2006-2-16

©2011 Walter de Gruyter GmbH & Co. KG, Berlin/Boston

Artikel in diesem Heft

  1. Article
  2. Low-Order Conditional Independence Graphs for Inferring Genetic Networks
  3. A Generalized Clustering Problem, with Application to DNA Microarrays
  4. A Bayes Regression Approach to Array-CGH Data
  5. Statistical Selection of Maintenance Genes for Normalization of Gene Expressions
  6. Predicting the Strongest Domain-Domain Contact in Interacting Protein Pairs
  7. Dimension Reduction for Classification with Gene Expression Microarray Data
  8. A New Type of Stochastic Dependence Revealed in Gene Expression Data
  9. A New Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity
  10. Quality Optimised Analysis of General Paired Microarray Experiments
  11. Issues of Processing and Multiple Testing of SELDI-TOF MS Proteomic Data
  12. Cross-Validated Bagged Prediction of Survival
  13. Treatment of Uninformative Families in Mean Allele Sharing Tests for Linkage
  14. Quantile-Function Based Null Distribution in Resampling Based Multiple Testing
  15. Combining Results of Microarray Experiments: A Rank Aggregation Approach
  16. Model Selection for Mixtures of Mutagenetic Trees
  17. Pseudo-likelihood for Non-reversible Nucleotide Substitution Models with Neighbour Dependent Rates
  18. A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting
  19. Bayesian Hierarchical Model for Correcting Signal Saturation in Microarrays Using Pixel Intensities
  20. Using Complexity for the Estimation of Bayesian Networks
  21. Detecting Local High-Scoring Segments: a First-Stage Approach for Genome-Wide Association Studies
  22. Examining Protein Structure and Similarities by Spectral Analysis Technique
  23. Parameter Estimation for the Exponential-Normal Convolution Model for Background Correction of Affymetrix GeneChip Data
  24. Approximate Sample Size Calculations with Microarray Data: An Illustration
  25. Numerical Solutions for Patterns Statistics on Markov Chains
  26. A Heuristic Bayesian Method for Segmenting DNA Sequence Alignments and Detecting Evidence for Recombination and Gene Conversion
  27. A Two-Step Multiple Comparison Procedure for a Large Number of Tests and Multiple Treatments
  28. Validation in Genomics: CpG Island Methylation Revisited
  29. An Improved Nonparametric Approach for Detecting Differentially Expressed Genes with Replicated Microarray Data
  30. Letter to the Editor
  31. Treating Expression Levels of Different Genes as a Sample in Microarray Data Analysis: Is it Worth a Risk?
  32. Reader's Reaction
  33. Reader's Reaction to "Dimension Reduction for Classification with Gene Expression Microarray Data" by Dai et al (2006)
https://doi.org/10.2202/1544-6115.1149
Schlagwörter für diesen Artikel
change point problem; comparative genomic hybridization; DNA copy number imbalance

Artikel in diesem Heft

  1. Article
  2. Low-Order Conditional Independence Graphs for Inferring Genetic Networks
  3. A Generalized Clustering Problem, with Application to DNA Microarrays
  4. A Bayes Regression Approach to Array-CGH Data
  5. Statistical Selection of Maintenance Genes for Normalization of Gene Expressions
  6. Predicting the Strongest Domain-Domain Contact in Interacting Protein Pairs
  7. Dimension Reduction for Classification with Gene Expression Microarray Data
  8. A New Type of Stochastic Dependence Revealed in Gene Expression Data
  9. A New Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity
  10. Quality Optimised Analysis of General Paired Microarray Experiments
  11. Issues of Processing and Multiple Testing of SELDI-TOF MS Proteomic Data
  12. Cross-Validated Bagged Prediction of Survival
  13. Treatment of Uninformative Families in Mean Allele Sharing Tests for Linkage
  14. Quantile-Function Based Null Distribution in Resampling Based Multiple Testing
  15. Combining Results of Microarray Experiments: A Rank Aggregation Approach
  16. Model Selection for Mixtures of Mutagenetic Trees
  17. Pseudo-likelihood for Non-reversible Nucleotide Substitution Models with Neighbour Dependent Rates
  18. A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting
  19. Bayesian Hierarchical Model for Correcting Signal Saturation in Microarrays Using Pixel Intensities
  20. Using Complexity for the Estimation of Bayesian Networks
  21. Detecting Local High-Scoring Segments: a First-Stage Approach for Genome-Wide Association Studies
  22. Examining Protein Structure and Similarities by Spectral Analysis Technique
  23. Parameter Estimation for the Exponential-Normal Convolution Model for Background Correction of Affymetrix GeneChip Data
  24. Approximate Sample Size Calculations with Microarray Data: An Illustration
  25. Numerical Solutions for Patterns Statistics on Markov Chains
  26. A Heuristic Bayesian Method for Segmenting DNA Sequence Alignments and Detecting Evidence for Recombination and Gene Conversion
  27. A Two-Step Multiple Comparison Procedure for a Large Number of Tests and Multiple Treatments
  28. Validation in Genomics: CpG Island Methylation Revisited
  29. An Improved Nonparametric Approach for Detecting Differentially Expressed Genes with Replicated Microarray Data
  30. Letter to the Editor
  31. Treating Expression Levels of Different Genes as a Sample in Microarray Data Analysis: Is it Worth a Risk?
  32. Reader's Reaction
  33. Reader's Reaction to "Dimension Reduction for Classification with Gene Expression Microarray Data" by Dai et al (2006)
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