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Numerical Solutions for Patterns Statistics on Markov Chains

  • Gregory Nuel
Published/Copyright: October 17, 2006
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Statistical Applications in Genetics and Molecular Biology
From the journal Statistical Applications in Genetics and Molecular Biology Volume 5 Issue 1

We propose here a review of the methods available to compute pattern statistics on text generated by a Markov source. Theoretical, but also numerical aspects are detailed for a wide range of techniques (exact, Gaussian, large deviations, binomial and compound Poisson). The SPatt package (Statistics for Pattern, free software available at http://stat.genopole.cnrs.fr/spatt) implementing all these methods is then used to compare all these approaches in terms of computational time and reliability in the most complete pattern statistics benchmark available at the present time.

Keywords: exact; Gaussian approximations; large deviations; compound Poisson approximations; benchmark
Published Online: 2006-10-17

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

Articles in the same Issue

  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/10.2202/1544-6115.1219
Keywords for this article
exact; Gaussian approximations; large deviations; compound Poisson approximations; benchmark

Articles in the same Issue

  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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