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Advances in statistical bioinformatics : models and integrative inference for high-throughput data / / edited by Kim-Anh Do, The University of Texas M.D. Anderson Cancer Center, Zhaohui Steven Qin, Emory University, Atlanta, GA, Marina Vannucci, Rice University, Houston, TX [[electronic resource]]
| Advances in statistical bioinformatics : models and integrative inference for high-throughput data / / edited by Kim-Anh Do, The University of Texas M.D. Anderson Cancer Center, Zhaohui Steven Qin, Emory University, Atlanta, GA, Marina Vannucci, Rice University, Houston, TX [[electronic resource]] |
| Pubbl/distr/stampa | Cambridge : , : Cambridge University Press, , 2013 |
| Descrizione fisica | 1 online resource (xv, 481 pages) : digital, PDF file(s) |
| Disciplina | 572.80285 |
| Soggetto topico |
Bioinformatics - Statistical methods
Biometry Genetics - Technique |
| ISBN |
1-139-89118-9
1-107-24941-4 1-107-24858-2 1-299-70751-3 1-107-25107-9 1-107-25024-2 1-139-22644-4 1-107-24775-6 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
""Contents""; ""List of Contributors""; ""Preface""; ""1 An Introduction to Next-Generation Biological Platforms""; ""Virginia Mohlere, Wenting Wang, and Ganiraju Manyam""; ""1.1 Introduction""; ""1.2 The Biology of Gene Silencing""; ""1.2.1 DNA Methylation""; ""1.2.2 RNA Interference""; ""1.3 High-Throughput Profiling""; ""1.3.1 Molecular Inversion Probe Arrays""; ""1.3.2 Array Comparative Genomic Hybridization (aCGH)""; ""1.3.3 Genome-Wide Association Studies""; ""1.3.4 Reverse-Phase Protein Array""; ""1.4 Next-Generation Sequencing""; ""1.4.1 Whole-Genome and Whole-Exome Sequencing""
""1.4.2 ChIP-Seq""""1.4.3 RNA-Seq""; ""1.4.4 BS-seq""; ""1.5 NGS Data Management and Analysis""; ""1.6 Platform Integration""; ""Acknowledgments""; ""References""; ""References""; ""2 An Introduction to The Cancer Genome Atlas""; ""Bradley M. Broom and Rehan Akbani""; ""2.1 Introduction""; ""2.2 History and Goals of the TCGA Project""; ""2.3 Sample Collection and Processing""; ""2.3.1 Step 1: Tissue Collection""; ""2.3.2 Step 2: Quality Control and DNA/RNA Extraction""; ""2.3.3 Step 3: Molecular Profiling and Sequencing""; ""2.3.4 Step 4: Data Collection and Public Distribution"" ""2.3.5 Step 5: Data Analysis""""2.4 Data Processing, Storage, and Access""; ""2.4.1 TCGA Barcodes and UUIDs""; ""2.4.2 The Data Coordinating Center""; ""2.4.3 Data Access Matrix""; ""2.4.4 Bulk Download""; ""2.4.5 HTTP""; ""2.4.6 CGHub""; ""2.4.7 Sample and Data Relationship Format (SDRF) and Investigation Description Format (IDF) Files""; ""2.4.8 File Format""; ""2.4.9 Version""; ""2.5 Tools for Visualizing and Analyzing TCGA Data""; ""2.5.1 cBio Cancer Genomics Portal""; ""2.5.2 MBatch Portal""; ""2.5.3 Next-Generation Clustered Heat Maps""; ""2.5.4 Regulome Explorer"" ""2.5.5 Integrative Genome Viewer""""2.5.6 Cancer Genomics Browser""; ""2.6 Summary""; ""Acknowledgments""; ""References""; ""References""; ""3 DNA Variant Calling in Targeted Sequencing Data""; ""Wenyi Wang, Yu Fan, and Terence P. Speed""; ""3.1 Introduction""; ""3.2 Background""; ""3.2.1 Single-Nucleotide Variation""; ""3.2.2 Long Padlock Probes""; ""3.2.3 Array-Based Resequencing""; ""3.3 Sequence Robust Multiarray Analysis""; ""3.3.1 Quality Control""; ""3.3.2 Variant Calling""; ""3.4 Application of SRMA""; ""3.4.1 Candidate Gene Study for Mitochondrial Diseases"" ""3.4.2 Validation Results""""3.4.3 Biological Findings""; ""3.5 Conclusion""; ""Appendix""; ""References""; ""References""; ""4 Statistical Analysis of Mapped Reads from mRNA-Seq Data""; ""Ernest Turro and Alex Lewin""; ""4.1 Background""; ""4.1.1 RNA Biology""; ""4.1.2 RNA Technology""; ""4.2 Mapping and Assembly Strategies""; ""4.2.1 De Novo Assembly of the Transcriptome""; ""4.2.2 Genome-Guided Assembly of the Transcriptome""; ""4.2.3 Alignment to a Reference Transcriptome""; ""4.3 Modeling Expression Levels""; ""4.3.1 Poisson Model for Expression Quantification""; ""4.4 Normalization"" ""4.4.1 RPKM Normalization"" |
| Record Nr. | UNINA-9910464935503321 |
| Cambridge : , : Cambridge University Press, , 2013 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Advances in statistical bioinformatics : models and integrative inference for high-throughput data / / edited by Kim-Anh Do, The University of Texas M.D. Anderson Cancer Center, Zhaohui Steven Qin, Emory University, Atlanta, GA, Marina Vannucci, Rice University, Houston, TX [[electronic resource]]
| Advances in statistical bioinformatics : models and integrative inference for high-throughput data / / edited by Kim-Anh Do, The University of Texas M.D. Anderson Cancer Center, Zhaohui Steven Qin, Emory University, Atlanta, GA, Marina Vannucci, Rice University, Houston, TX [[electronic resource]] |
| Pubbl/distr/stampa | Cambridge : , : Cambridge University Press, , 2013 |
| Descrizione fisica | 1 online resource (xv, 481 pages) : digital, PDF file(s) |
| Disciplina | 572.80285 |
| Soggetto topico |
Bioinformatics - Statistical methods
Biometry Genetics - Technique |
| ISBN |
1-139-89118-9
1-107-24941-4 1-107-24858-2 1-299-70751-3 1-107-25107-9 1-107-25024-2 1-139-22644-4 1-107-24775-6 |
| Classificazione | MED090000 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
""Contents""; ""List of Contributors""; ""Preface""; ""1 An Introduction to Next-Generation Biological Platforms""; ""Virginia Mohlere, Wenting Wang, and Ganiraju Manyam""; ""1.1 Introduction""; ""1.2 The Biology of Gene Silencing""; ""1.2.1 DNA Methylation""; ""1.2.2 RNA Interference""; ""1.3 High-Throughput Profiling""; ""1.3.1 Molecular Inversion Probe Arrays""; ""1.3.2 Array Comparative Genomic Hybridization (aCGH)""; ""1.3.3 Genome-Wide Association Studies""; ""1.3.4 Reverse-Phase Protein Array""; ""1.4 Next-Generation Sequencing""; ""1.4.1 Whole-Genome and Whole-Exome Sequencing""
""1.4.2 ChIP-Seq""""1.4.3 RNA-Seq""; ""1.4.4 BS-seq""; ""1.5 NGS Data Management and Analysis""; ""1.6 Platform Integration""; ""Acknowledgments""; ""References""; ""References""; ""2 An Introduction to The Cancer Genome Atlas""; ""Bradley M. Broom and Rehan Akbani""; ""2.1 Introduction""; ""2.2 History and Goals of the TCGA Project""; ""2.3 Sample Collection and Processing""; ""2.3.1 Step 1: Tissue Collection""; ""2.3.2 Step 2: Quality Control and DNA/RNA Extraction""; ""2.3.3 Step 3: Molecular Profiling and Sequencing""; ""2.3.4 Step 4: Data Collection and Public Distribution"" ""2.3.5 Step 5: Data Analysis""""2.4 Data Processing, Storage, and Access""; ""2.4.1 TCGA Barcodes and UUIDs""; ""2.4.2 The Data Coordinating Center""; ""2.4.3 Data Access Matrix""; ""2.4.4 Bulk Download""; ""2.4.5 HTTP""; ""2.4.6 CGHub""; ""2.4.7 Sample and Data Relationship Format (SDRF) and Investigation Description Format (IDF) Files""; ""2.4.8 File Format""; ""2.4.9 Version""; ""2.5 Tools for Visualizing and Analyzing TCGA Data""; ""2.5.1 cBio Cancer Genomics Portal""; ""2.5.2 MBatch Portal""; ""2.5.3 Next-Generation Clustered Heat Maps""; ""2.5.4 Regulome Explorer"" ""2.5.5 Integrative Genome Viewer""""2.5.6 Cancer Genomics Browser""; ""2.6 Summary""; ""Acknowledgments""; ""References""; ""References""; ""3 DNA Variant Calling in Targeted Sequencing Data""; ""Wenyi Wang, Yu Fan, and Terence P. Speed""; ""3.1 Introduction""; ""3.2 Background""; ""3.2.1 Single-Nucleotide Variation""; ""3.2.2 Long Padlock Probes""; ""3.2.3 Array-Based Resequencing""; ""3.3 Sequence Robust Multiarray Analysis""; ""3.3.1 Quality Control""; ""3.3.2 Variant Calling""; ""3.4 Application of SRMA""; ""3.4.1 Candidate Gene Study for Mitochondrial Diseases"" ""3.4.2 Validation Results""""3.4.3 Biological Findings""; ""3.5 Conclusion""; ""Appendix""; ""References""; ""References""; ""4 Statistical Analysis of Mapped Reads from mRNA-Seq Data""; ""Ernest Turro and Alex Lewin""; ""4.1 Background""; ""4.1.1 RNA Biology""; ""4.1.2 RNA Technology""; ""4.2 Mapping and Assembly Strategies""; ""4.2.1 De Novo Assembly of the Transcriptome""; ""4.2.2 Genome-Guided Assembly of the Transcriptome""; ""4.2.3 Alignment to a Reference Transcriptome""; ""4.3 Modeling Expression Levels""; ""4.3.1 Poisson Model for Expression Quantification""; ""4.4 Normalization"" ""4.4.1 RPKM Normalization"" |
| Record Nr. | UNINA-9910789313903321 |
| Cambridge : , : Cambridge University Press, , 2013 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Advances in statistical bioinformatics : models and integrative inference for high-throughput data / / edited by Kim-Anh Do, The University of Texas M.D. Anderson Cancer Center, Zhaohui Steven Qin, Emory University, Atlanta, GA, Marina Vannucci, Rice University, Houston, TX [[electronic resource]]
| Advances in statistical bioinformatics : models and integrative inference for high-throughput data / / edited by Kim-Anh Do, The University of Texas M.D. Anderson Cancer Center, Zhaohui Steven Qin, Emory University, Atlanta, GA, Marina Vannucci, Rice University, Houston, TX [[electronic resource]] |
| Pubbl/distr/stampa | Cambridge : , : Cambridge University Press, , 2013 |
| Descrizione fisica | 1 online resource (xv, 481 pages) : digital, PDF file(s) |
| Disciplina | 572.80285 |
| Soggetto topico |
Bioinformatics - Statistical methods
Biometry Genetics - Technique |
| ISBN |
1-139-89118-9
1-107-24941-4 1-107-24858-2 1-299-70751-3 1-107-25107-9 1-107-25024-2 1-139-22644-4 1-107-24775-6 |
| Classificazione | MED090000 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
""Contents""; ""List of Contributors""; ""Preface""; ""1 An Introduction to Next-Generation Biological Platforms""; ""Virginia Mohlere, Wenting Wang, and Ganiraju Manyam""; ""1.1 Introduction""; ""1.2 The Biology of Gene Silencing""; ""1.2.1 DNA Methylation""; ""1.2.2 RNA Interference""; ""1.3 High-Throughput Profiling""; ""1.3.1 Molecular Inversion Probe Arrays""; ""1.3.2 Array Comparative Genomic Hybridization (aCGH)""; ""1.3.3 Genome-Wide Association Studies""; ""1.3.4 Reverse-Phase Protein Array""; ""1.4 Next-Generation Sequencing""; ""1.4.1 Whole-Genome and Whole-Exome Sequencing""
""1.4.2 ChIP-Seq""""1.4.3 RNA-Seq""; ""1.4.4 BS-seq""; ""1.5 NGS Data Management and Analysis""; ""1.6 Platform Integration""; ""Acknowledgments""; ""References""; ""References""; ""2 An Introduction to The Cancer Genome Atlas""; ""Bradley M. Broom and Rehan Akbani""; ""2.1 Introduction""; ""2.2 History and Goals of the TCGA Project""; ""2.3 Sample Collection and Processing""; ""2.3.1 Step 1: Tissue Collection""; ""2.3.2 Step 2: Quality Control and DNA/RNA Extraction""; ""2.3.3 Step 3: Molecular Profiling and Sequencing""; ""2.3.4 Step 4: Data Collection and Public Distribution"" ""2.3.5 Step 5: Data Analysis""""2.4 Data Processing, Storage, and Access""; ""2.4.1 TCGA Barcodes and UUIDs""; ""2.4.2 The Data Coordinating Center""; ""2.4.3 Data Access Matrix""; ""2.4.4 Bulk Download""; ""2.4.5 HTTP""; ""2.4.6 CGHub""; ""2.4.7 Sample and Data Relationship Format (SDRF) and Investigation Description Format (IDF) Files""; ""2.4.8 File Format""; ""2.4.9 Version""; ""2.5 Tools for Visualizing and Analyzing TCGA Data""; ""2.5.1 cBio Cancer Genomics Portal""; ""2.5.2 MBatch Portal""; ""2.5.3 Next-Generation Clustered Heat Maps""; ""2.5.4 Regulome Explorer"" ""2.5.5 Integrative Genome Viewer""""2.5.6 Cancer Genomics Browser""; ""2.6 Summary""; ""Acknowledgments""; ""References""; ""References""; ""3 DNA Variant Calling in Targeted Sequencing Data""; ""Wenyi Wang, Yu Fan, and Terence P. Speed""; ""3.1 Introduction""; ""3.2 Background""; ""3.2.1 Single-Nucleotide Variation""; ""3.2.2 Long Padlock Probes""; ""3.2.3 Array-Based Resequencing""; ""3.3 Sequence Robust Multiarray Analysis""; ""3.3.1 Quality Control""; ""3.3.2 Variant Calling""; ""3.4 Application of SRMA""; ""3.4.1 Candidate Gene Study for Mitochondrial Diseases"" ""3.4.2 Validation Results""""3.4.3 Biological Findings""; ""3.5 Conclusion""; ""Appendix""; ""References""; ""References""; ""4 Statistical Analysis of Mapped Reads from mRNA-Seq Data""; ""Ernest Turro and Alex Lewin""; ""4.1 Background""; ""4.1.1 RNA Biology""; ""4.1.2 RNA Technology""; ""4.2 Mapping and Assembly Strategies""; ""4.2.1 De Novo Assembly of the Transcriptome""; ""4.2.2 Genome-Guided Assembly of the Transcriptome""; ""4.2.3 Alignment to a Reference Transcriptome""; ""4.3 Modeling Expression Levels""; ""4.3.1 Poisson Model for Expression Quantification""; ""4.4 Normalization"" ""4.4.1 RPKM Normalization"" |
| Record Nr. | UNINA-9910810575303321 |
| Cambridge : , : Cambridge University Press, , 2013 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Analyzing microarray gene expression data [[electronic resource] /] / Geoffrey J. McLachlan, Kim-Anh Do, Christopher Ambroise
| Analyzing microarray gene expression data [[electronic resource] /] / Geoffrey J. McLachlan, Kim-Anh Do, Christopher Ambroise |
| Autore | McLachlan Geoffrey J. <1946-> |
| Pubbl/distr/stampa | Hoboken, N.J., : Wiley-Interscience, c2004 |
| Descrizione fisica | 1 online resource (366 p.) |
| Disciplina |
572.8636
572.865 |
| Altri autori (Persone) |
DoKim-Anh <1960->
AmbroiseChristophe <1969-> |
| Collana | Wiley series in probability and statistics |
| Soggetto topico |
DNA microarrays - Statistical methods
Gene expression - Statistical methods |
| Soggetto genere / forma | Electronic books. |
| ISBN |
1-280-25332-0
9786610253326 0-470-35030-X 0-471-72612-5 0-471-72842-X |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Analyzing Microarray Gene Expression Data; Contents; Preface; 1 Microarrays in Gene Expression Studies; 1.1 Introduction; 1.2 Background Biology; 1.2.1 Genome, Genotype, and Gene Expression; 1.2.2 Of Wild-Types and Other Alleles; 1.2.3 Aspects of Underlying Biology and Physiochemistry; 1.3 Polymerase Chain Reaction; 1.4 cDNA; 1.4.1 Expressed Sequence Tag; 1.5 Microarray Technology and Application; 1.5.1 History of Microarray Development; 1.5.2 Tools of Microarray Technology; 1.5.3 Limitations of Microarray Technology; 1.5.4 Oligonucleotides versus cDNA Arrays
1.5.5 SAGE: Another Method for Detecting and Measuring Gene Expression Levels1.5.6 Emerging Technologies; 1.6 Sampling of Relevant Research Entities and Public Resources; 2 Cleaning and Normalization; 2.1 Introduction; 2.2 Cleaning Procedures; 2.2.1 Image Processing to Extract Information; 2.2.2 Missing Value Estimation; 2.2.3 Sources of Nonlinearity; 2.3 Normalization and Plotting Procedures for Oligonucleotide Arrays; 2.3.1 Global Approaches for Oligonucleotide Array Data; 2.3.2 Spiked Standard Approaches; 2.3.3 Geometric Mean and Linear Regression Normalization for Multiple Arrays 2.3.4 Nonlinear Normalization for Multiple Arrays Using Smooth Curves2.4 Normalization Methods for cDNA Microarray Data; 2.4.1 Single-Array Normalization; 2.4.2 Multiple Slides Normalization; 2.4.3 ANOVA and Related Methods for Normalization; 2.4.4 Mixed-Model Method for Normalization; 2.4.5 SNOMAD; 2.5 Transformations and Replication; 2.5.1 Importance of Replication; 2.5.2 Transformations; 2.6 Analysis of the Alon Data Set; 2.7 Comparison of Normalization Strategies and Discussion; 3 Some Cluster Analysis Methods; 3.1 Introduction; 3.2 Reduction in the Dimension of the Feature Space 3.3 Cluster Analysis3.4 Some Hierarchical Agglomerative Techniques; 3.5 k-Means Clustering; 3.6 Cluster Analysis with No A Priori Metric; 3.7 Clustering via Finite Mixture Models; 3.7.1 Definition; 3.7.2 Advantages of Model-Based Clustering; 3.8 Fitting Mixture Models Via the EM Algorithm; 3.8.1 E-Step; 3.8.2 M-Step; 3.8.3 Choice of Starting Values for the EM Algorithm; 3.9 Clustering Via Normal Mixtures; 3.9.1 Heteroscedastic Components; 3.9.2 Homoscedastic Components; 3.9.3 Spherical Components; 3.9.4 Choice of Root; 3.9.5 Available Software; 3.10 Mixtures of t Distributions 3.11 Mixtures of Factor Analyzers3.12 Choice of Clustering Solution; 3.13 Classification ML Approach; 3.14 Mixture Models for Clinical and Microarray Data; 3.14.1 Unconditional Approach; 3.14.2 Conditional Approach; 3.15 Choice of the Number of Components in a Mixture Model; 3.15.1 Order of a Mixture Model; 3.15.2 Approaches for Assessing Mixture Order; 3.15.3 Bayesian Information Criterion; 3.15.4 Integrated Classification Likelihood Criterion; 3.16 Resampling Approach; 3.17 Other Resampling Approaches for Number of Clusters; 3.17.1 The Gap Statistic 3.17.2 The Clest Method for the Number of Clusters |
| Record Nr. | UNINA-9910146082203321 |
McLachlan Geoffrey J. <1946->
|
||
| Hoboken, N.J., : Wiley-Interscience, c2004 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Analyzing microarray gene expression data [[electronic resource] /] / Geoffrey J. McLachlan, Kim-Anh Do, Christopher Ambroise
| Analyzing microarray gene expression data [[electronic resource] /] / Geoffrey J. McLachlan, Kim-Anh Do, Christopher Ambroise |
| Autore | McLachlan Geoffrey J. <1946-> |
| Pubbl/distr/stampa | Hoboken, N.J., : Wiley-Interscience, c2004 |
| Descrizione fisica | 1 online resource (366 p.) |
| Disciplina |
572.8636
572.865 |
| Altri autori (Persone) |
DoKim-Anh <1960->
AmbroiseChristophe <1969-> |
| Collana | Wiley series in probability and statistics |
| Soggetto topico |
DNA microarrays - Statistical methods
Gene expression - Statistical methods |
| ISBN |
1-280-25332-0
9786610253326 0-470-35030-X 0-471-72612-5 0-471-72842-X |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Analyzing Microarray Gene Expression Data; Contents; Preface; 1 Microarrays in Gene Expression Studies; 1.1 Introduction; 1.2 Background Biology; 1.2.1 Genome, Genotype, and Gene Expression; 1.2.2 Of Wild-Types and Other Alleles; 1.2.3 Aspects of Underlying Biology and Physiochemistry; 1.3 Polymerase Chain Reaction; 1.4 cDNA; 1.4.1 Expressed Sequence Tag; 1.5 Microarray Technology and Application; 1.5.1 History of Microarray Development; 1.5.2 Tools of Microarray Technology; 1.5.3 Limitations of Microarray Technology; 1.5.4 Oligonucleotides versus cDNA Arrays
1.5.5 SAGE: Another Method for Detecting and Measuring Gene Expression Levels1.5.6 Emerging Technologies; 1.6 Sampling of Relevant Research Entities and Public Resources; 2 Cleaning and Normalization; 2.1 Introduction; 2.2 Cleaning Procedures; 2.2.1 Image Processing to Extract Information; 2.2.2 Missing Value Estimation; 2.2.3 Sources of Nonlinearity; 2.3 Normalization and Plotting Procedures for Oligonucleotide Arrays; 2.3.1 Global Approaches for Oligonucleotide Array Data; 2.3.2 Spiked Standard Approaches; 2.3.3 Geometric Mean and Linear Regression Normalization for Multiple Arrays 2.3.4 Nonlinear Normalization for Multiple Arrays Using Smooth Curves2.4 Normalization Methods for cDNA Microarray Data; 2.4.1 Single-Array Normalization; 2.4.2 Multiple Slides Normalization; 2.4.3 ANOVA and Related Methods for Normalization; 2.4.4 Mixed-Model Method for Normalization; 2.4.5 SNOMAD; 2.5 Transformations and Replication; 2.5.1 Importance of Replication; 2.5.2 Transformations; 2.6 Analysis of the Alon Data Set; 2.7 Comparison of Normalization Strategies and Discussion; 3 Some Cluster Analysis Methods; 3.1 Introduction; 3.2 Reduction in the Dimension of the Feature Space 3.3 Cluster Analysis3.4 Some Hierarchical Agglomerative Techniques; 3.5 k-Means Clustering; 3.6 Cluster Analysis with No A Priori Metric; 3.7 Clustering via Finite Mixture Models; 3.7.1 Definition; 3.7.2 Advantages of Model-Based Clustering; 3.8 Fitting Mixture Models Via the EM Algorithm; 3.8.1 E-Step; 3.8.2 M-Step; 3.8.3 Choice of Starting Values for the EM Algorithm; 3.9 Clustering Via Normal Mixtures; 3.9.1 Heteroscedastic Components; 3.9.2 Homoscedastic Components; 3.9.3 Spherical Components; 3.9.4 Choice of Root; 3.9.5 Available Software; 3.10 Mixtures of t Distributions 3.11 Mixtures of Factor Analyzers3.12 Choice of Clustering Solution; 3.13 Classification ML Approach; 3.14 Mixture Models for Clinical and Microarray Data; 3.14.1 Unconditional Approach; 3.14.2 Conditional Approach; 3.15 Choice of the Number of Components in a Mixture Model; 3.15.1 Order of a Mixture Model; 3.15.2 Approaches for Assessing Mixture Order; 3.15.3 Bayesian Information Criterion; 3.15.4 Integrated Classification Likelihood Criterion; 3.16 Resampling Approach; 3.17 Other Resampling Approaches for Number of Clusters; 3.17.1 The Gap Statistic 3.17.2 The Clest Method for the Number of Clusters |
| Record Nr. | UNINA-9910830637803321 |
|
McLachlan Geoffrey J. <1946->
|
||
| Hoboken, N.J., : Wiley-Interscience, c2004 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Analyzing microarray gene expression data [[electronic resource] /] / Geoffrey J. McLachlan, Kim-Anh Do, Christopher Ambroise
| Analyzing microarray gene expression data [[electronic resource] /] / Geoffrey J. McLachlan, Kim-Anh Do, Christopher Ambroise |
| Autore | McLachlan Geoffrey J. <1946-> |
| Pubbl/distr/stampa | Hoboken, N.J., : Wiley-Interscience, c2004 |
| Descrizione fisica | 1 online resource (366 p.) |
| Disciplina |
572.8636
572.865 |
| Altri autori (Persone) |
DoKim-Anh <1960->
AmbroiseChristophe <1969-> |
| Collana | Wiley series in probability and statistics |
| Soggetto topico |
DNA microarrays - Statistical methods
Gene expression - Statistical methods |
| ISBN |
1-280-25332-0
9786610253326 0-470-35030-X 0-471-72612-5 0-471-72842-X |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Analyzing Microarray Gene Expression Data; Contents; Preface; 1 Microarrays in Gene Expression Studies; 1.1 Introduction; 1.2 Background Biology; 1.2.1 Genome, Genotype, and Gene Expression; 1.2.2 Of Wild-Types and Other Alleles; 1.2.3 Aspects of Underlying Biology and Physiochemistry; 1.3 Polymerase Chain Reaction; 1.4 cDNA; 1.4.1 Expressed Sequence Tag; 1.5 Microarray Technology and Application; 1.5.1 History of Microarray Development; 1.5.2 Tools of Microarray Technology; 1.5.3 Limitations of Microarray Technology; 1.5.4 Oligonucleotides versus cDNA Arrays
1.5.5 SAGE: Another Method for Detecting and Measuring Gene Expression Levels1.5.6 Emerging Technologies; 1.6 Sampling of Relevant Research Entities and Public Resources; 2 Cleaning and Normalization; 2.1 Introduction; 2.2 Cleaning Procedures; 2.2.1 Image Processing to Extract Information; 2.2.2 Missing Value Estimation; 2.2.3 Sources of Nonlinearity; 2.3 Normalization and Plotting Procedures for Oligonucleotide Arrays; 2.3.1 Global Approaches for Oligonucleotide Array Data; 2.3.2 Spiked Standard Approaches; 2.3.3 Geometric Mean and Linear Regression Normalization for Multiple Arrays 2.3.4 Nonlinear Normalization for Multiple Arrays Using Smooth Curves2.4 Normalization Methods for cDNA Microarray Data; 2.4.1 Single-Array Normalization; 2.4.2 Multiple Slides Normalization; 2.4.3 ANOVA and Related Methods for Normalization; 2.4.4 Mixed-Model Method for Normalization; 2.4.5 SNOMAD; 2.5 Transformations and Replication; 2.5.1 Importance of Replication; 2.5.2 Transformations; 2.6 Analysis of the Alon Data Set; 2.7 Comparison of Normalization Strategies and Discussion; 3 Some Cluster Analysis Methods; 3.1 Introduction; 3.2 Reduction in the Dimension of the Feature Space 3.3 Cluster Analysis3.4 Some Hierarchical Agglomerative Techniques; 3.5 k-Means Clustering; 3.6 Cluster Analysis with No A Priori Metric; 3.7 Clustering via Finite Mixture Models; 3.7.1 Definition; 3.7.2 Advantages of Model-Based Clustering; 3.8 Fitting Mixture Models Via the EM Algorithm; 3.8.1 E-Step; 3.8.2 M-Step; 3.8.3 Choice of Starting Values for the EM Algorithm; 3.9 Clustering Via Normal Mixtures; 3.9.1 Heteroscedastic Components; 3.9.2 Homoscedastic Components; 3.9.3 Spherical Components; 3.9.4 Choice of Root; 3.9.5 Available Software; 3.10 Mixtures of t Distributions 3.11 Mixtures of Factor Analyzers3.12 Choice of Clustering Solution; 3.13 Classification ML Approach; 3.14 Mixture Models for Clinical and Microarray Data; 3.14.1 Unconditional Approach; 3.14.2 Conditional Approach; 3.15 Choice of the Number of Components in a Mixture Model; 3.15.1 Order of a Mixture Model; 3.15.2 Approaches for Assessing Mixture Order; 3.15.3 Bayesian Information Criterion; 3.15.4 Integrated Classification Likelihood Criterion; 3.16 Resampling Approach; 3.17 Other Resampling Approaches for Number of Clusters; 3.17.1 The Gap Statistic 3.17.2 The Clest Method for the Number of Clusters |
| Record Nr. | UNINA-9910840946603321 |
|
McLachlan Geoffrey J. <1946->
|
||
| Hoboken, N.J., : Wiley-Interscience, c2004 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||