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Guide to analysis of DNA microarray data [[electronic resource] /] / Steen Knudsen
| Guide to analysis of DNA microarray data [[electronic resource] /] / Steen Knudsen |
| Autore | Knudsen Steen |
| Edizione | [2nd ed.] |
| Pubbl/distr/stampa | Hoboken, N.J., : Wiley-Liss, c2004 |
| Descrizione fisica | 1 online resource (194 p.) |
| Disciplina |
572.86
572.8636 |
| Altri autori (Persone) | KnudsenSteen |
| Soggetto topico | DNA microarrays |
| Soggetto genere / forma | Electronic books. |
| ISBN |
1-280-25320-7
9786610253203 0-471-67026-X 0-471-67027-8 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Guide to ANALYSIS OF DNA MICROARRAY DATA; Contents; Preface; Acknowledgments; 1 Introduction to DNA Microarray Technology; 1.1 Hybridization; 1.2 Gold Rush?; 1.3 The Technology Behind DNA Microarrays; 1.3.1 Affymetrix GeneChip Technology; 1.3.2 Spotted Arrays; 1.3.3 Digital Micromirror Arrays; 1.3.4 Inkjet Arrays; 1.3.5 Bead Arrays; 1.3.6 Serial Analysis of Gene Expression (SAGE); 1.4 Parallel Sequencing on Microbead Arrays; 1.4.1 Emerging Technologies; 1.5 Example: Affymetrix vs. Spotted Arrays; 1.6 Summary; 1.7 Further Reading; 2 Overview of Data Analysis; 3 Image Analysis; 3.1 Gridding
3.2 Segmentation3.3 Intensity Extraction; 3.4 Background Correction; 3.5 Software; 3.5.1 Free Software for Array Image Analysis; 3.5.2 Commercial Software for Array Image Analysis; 3.6 Summary; 3.7 Further Reading; 4 Basic Data Analysis; 4.1 Normalization; 4.1.1 One or More Genes Assumed Expressed at Constant Rate; 4.1.2 Sum of Genes is Assumed Constant; 4.1.3 Subset of Genes is Assumed Constant; 4.1.4 Majority of Genes Assumed Constant; 4.1.5 Spike Controls; 4.2 Dye Bias, Spatial Bias, Print Tip Bias; 4.3 Expression Indices; 4.3.1 Average Difference; 4.3.2 Signal 4.3.3 Model-Based Expression Index4.3.4 Robust Multiarray Average; 4.3.5 Position Dependent Nearest Neighbor Model; 4.4 Detection of Outliers; 4.5 Fold Change; 4.6 Significance; 4.6.1 Multiple Conditions; 4.6.2 Nonparametric Tests; 4.6.3 Correction for Multiple Testing; 4.6.4 Example I: t-Test and ANOVA; 4.6.5 Example II: Number of Replicates; 4.7 Mixed Cell Populations; 4.8 Summary; 4.9 Further Reading; 5 Visualization by Reduction of Dimensionality; 5.1 Principal Component Analysis; 5.2 Example 1: PCA on Small Data Matrix; 5.3 Example 2: PCA on Real Data; 5.4 Summary; 5.5 Further Reading 6 Cluster Analysis6.1 Hierarchical Clustering; 6.2 K-means Clustering; 6.3 Self-organizing Maps; 6.4 Distance Measures; 6.4.1 Example: Comparison of Distance Measures; 6.5 Time-Series Analysis; 6.6 Gene Normalization; 6.7 Visualization of Clusters; 6.7.1 Example: Visualization of Gene Clusters in Bladder Cancer; 6.8 Summary; 6.9 Further Reading; 7 Beyond Cluster Analysis; 7.1 Function Prediction; 7.2 Discovery of Regulatory Elements in Promoter Regions; 7.2.1 Example 1: Discovery of Proteasomal Element; 7.2.2 Example 2: Rediscovery of Mlu Cell Cycle Box (MCB); 7.3 Summary; 7.4 Further Reading 8 Automated Analysis, Integrated Analysis, and Systems Biology8.1 Integrated Analysis; 8.2 Systems Biology; 8.3 Further Reading; 9 Reverse Engineering of Regulatory Networks; 9.1 The Time-Series Approach; 9.2 The Steady-State Approach; 9.3 Limitations of Network Modeling; 9.4 Example 1: Steady-State Model; 9.5 Example 2: Steady-State Model on Bacillus Data; 9.6 Example 3: Linear Time-Series Model; 9.7 Further Reading; 10 Molecular Classifiers; 10.1 Feature Selection; 10.2 Validation; 10.3 Classification Schemes; 10.3.1 Nearest Neighbor; 10.3.2 Nearest Centroid; 10.3.3 Neural Networks 10.3.4 Support Vector Machine |
| Altri titoli varianti | Analysis of DNA microarray data |
| Record Nr. | UNINA-9910146073503321 |
Knudsen Steen
|
||
| Hoboken, N.J., : Wiley-Liss, c2004 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Guide to analysis of DNA microarray data [[electronic resource] /] / Steen Knudsen
| Guide to analysis of DNA microarray data [[electronic resource] /] / Steen Knudsen |
| Autore | Knudsen Steen |
| Edizione | [2nd ed.] |
| Pubbl/distr/stampa | Hoboken, N.J., : Wiley-Liss, c2004 |
| Descrizione fisica | 1 online resource (194 p.) |
| Disciplina |
572.86
572.8636 |
| Altri autori (Persone) | KnudsenSteen |
| Soggetto topico | DNA microarrays |
| ISBN |
1-280-25320-7
9786610253203 0-471-67026-X 0-471-67027-8 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Guide to ANALYSIS OF DNA MICROARRAY DATA; Contents; Preface; Acknowledgments; 1 Introduction to DNA Microarray Technology; 1.1 Hybridization; 1.2 Gold Rush?; 1.3 The Technology Behind DNA Microarrays; 1.3.1 Affymetrix GeneChip Technology; 1.3.2 Spotted Arrays; 1.3.3 Digital Micromirror Arrays; 1.3.4 Inkjet Arrays; 1.3.5 Bead Arrays; 1.3.6 Serial Analysis of Gene Expression (SAGE); 1.4 Parallel Sequencing on Microbead Arrays; 1.4.1 Emerging Technologies; 1.5 Example: Affymetrix vs. Spotted Arrays; 1.6 Summary; 1.7 Further Reading; 2 Overview of Data Analysis; 3 Image Analysis; 3.1 Gridding
3.2 Segmentation3.3 Intensity Extraction; 3.4 Background Correction; 3.5 Software; 3.5.1 Free Software for Array Image Analysis; 3.5.2 Commercial Software for Array Image Analysis; 3.6 Summary; 3.7 Further Reading; 4 Basic Data Analysis; 4.1 Normalization; 4.1.1 One or More Genes Assumed Expressed at Constant Rate; 4.1.2 Sum of Genes is Assumed Constant; 4.1.3 Subset of Genes is Assumed Constant; 4.1.4 Majority of Genes Assumed Constant; 4.1.5 Spike Controls; 4.2 Dye Bias, Spatial Bias, Print Tip Bias; 4.3 Expression Indices; 4.3.1 Average Difference; 4.3.2 Signal 4.3.3 Model-Based Expression Index4.3.4 Robust Multiarray Average; 4.3.5 Position Dependent Nearest Neighbor Model; 4.4 Detection of Outliers; 4.5 Fold Change; 4.6 Significance; 4.6.1 Multiple Conditions; 4.6.2 Nonparametric Tests; 4.6.3 Correction for Multiple Testing; 4.6.4 Example I: t-Test and ANOVA; 4.6.5 Example II: Number of Replicates; 4.7 Mixed Cell Populations; 4.8 Summary; 4.9 Further Reading; 5 Visualization by Reduction of Dimensionality; 5.1 Principal Component Analysis; 5.2 Example 1: PCA on Small Data Matrix; 5.3 Example 2: PCA on Real Data; 5.4 Summary; 5.5 Further Reading 6 Cluster Analysis6.1 Hierarchical Clustering; 6.2 K-means Clustering; 6.3 Self-organizing Maps; 6.4 Distance Measures; 6.4.1 Example: Comparison of Distance Measures; 6.5 Time-Series Analysis; 6.6 Gene Normalization; 6.7 Visualization of Clusters; 6.7.1 Example: Visualization of Gene Clusters in Bladder Cancer; 6.8 Summary; 6.9 Further Reading; 7 Beyond Cluster Analysis; 7.1 Function Prediction; 7.2 Discovery of Regulatory Elements in Promoter Regions; 7.2.1 Example 1: Discovery of Proteasomal Element; 7.2.2 Example 2: Rediscovery of Mlu Cell Cycle Box (MCB); 7.3 Summary; 7.4 Further Reading 8 Automated Analysis, Integrated Analysis, and Systems Biology8.1 Integrated Analysis; 8.2 Systems Biology; 8.3 Further Reading; 9 Reverse Engineering of Regulatory Networks; 9.1 The Time-Series Approach; 9.2 The Steady-State Approach; 9.3 Limitations of Network Modeling; 9.4 Example 1: Steady-State Model; 9.5 Example 2: Steady-State Model on Bacillus Data; 9.6 Example 3: Linear Time-Series Model; 9.7 Further Reading; 10 Molecular Classifiers; 10.1 Feature Selection; 10.2 Validation; 10.3 Classification Schemes; 10.3.1 Nearest Neighbor; 10.3.2 Nearest Centroid; 10.3.3 Neural Networks 10.3.4 Support Vector Machine |
| Altri titoli varianti | Analysis of DNA microarray data |
| Record Nr. | UNINA-9910830332603321 |
|
Knudsen Steen
|
||
| Hoboken, N.J., : Wiley-Liss, c2004 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Guide to analysis of DNA microarray data / / Steen Knudsen
| Guide to analysis of DNA microarray data / / Steen Knudsen |
| Autore | Knudsen Steen |
| Edizione | [2nd ed.] |
| Pubbl/distr/stampa | Hoboken, N.J., : Wiley-Liss, c2004 |
| Descrizione fisica | 1 online resource (194 p.) |
| Disciplina | 572.8/636 |
| Altri autori (Persone) | KnudsenSteen |
| Soggetto topico | DNA microarrays |
| ISBN |
1-280-25320-7
9786610253203 0-471-67026-X 0-471-67027-8 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Guide to ANALYSIS OF DNA MICROARRAY DATA; Contents; Preface; Acknowledgments; 1 Introduction to DNA Microarray Technology; 1.1 Hybridization; 1.2 Gold Rush?; 1.3 The Technology Behind DNA Microarrays; 1.3.1 Affymetrix GeneChip Technology; 1.3.2 Spotted Arrays; 1.3.3 Digital Micromirror Arrays; 1.3.4 Inkjet Arrays; 1.3.5 Bead Arrays; 1.3.6 Serial Analysis of Gene Expression (SAGE); 1.4 Parallel Sequencing on Microbead Arrays; 1.4.1 Emerging Technologies; 1.5 Example: Affymetrix vs. Spotted Arrays; 1.6 Summary; 1.7 Further Reading; 2 Overview of Data Analysis; 3 Image Analysis; 3.1 Gridding
3.2 Segmentation3.3 Intensity Extraction; 3.4 Background Correction; 3.5 Software; 3.5.1 Free Software for Array Image Analysis; 3.5.2 Commercial Software for Array Image Analysis; 3.6 Summary; 3.7 Further Reading; 4 Basic Data Analysis; 4.1 Normalization; 4.1.1 One or More Genes Assumed Expressed at Constant Rate; 4.1.2 Sum of Genes is Assumed Constant; 4.1.3 Subset of Genes is Assumed Constant; 4.1.4 Majority of Genes Assumed Constant; 4.1.5 Spike Controls; 4.2 Dye Bias, Spatial Bias, Print Tip Bias; 4.3 Expression Indices; 4.3.1 Average Difference; 4.3.2 Signal 4.3.3 Model-Based Expression Index4.3.4 Robust Multiarray Average; 4.3.5 Position Dependent Nearest Neighbor Model; 4.4 Detection of Outliers; 4.5 Fold Change; 4.6 Significance; 4.6.1 Multiple Conditions; 4.6.2 Nonparametric Tests; 4.6.3 Correction for Multiple Testing; 4.6.4 Example I: t-Test and ANOVA; 4.6.5 Example II: Number of Replicates; 4.7 Mixed Cell Populations; 4.8 Summary; 4.9 Further Reading; 5 Visualization by Reduction of Dimensionality; 5.1 Principal Component Analysis; 5.2 Example 1: PCA on Small Data Matrix; 5.3 Example 2: PCA on Real Data; 5.4 Summary; 5.5 Further Reading 6 Cluster Analysis6.1 Hierarchical Clustering; 6.2 K-means Clustering; 6.3 Self-organizing Maps; 6.4 Distance Measures; 6.4.1 Example: Comparison of Distance Measures; 6.5 Time-Series Analysis; 6.6 Gene Normalization; 6.7 Visualization of Clusters; 6.7.1 Example: Visualization of Gene Clusters in Bladder Cancer; 6.8 Summary; 6.9 Further Reading; 7 Beyond Cluster Analysis; 7.1 Function Prediction; 7.2 Discovery of Regulatory Elements in Promoter Regions; 7.2.1 Example 1: Discovery of Proteasomal Element; 7.2.2 Example 2: Rediscovery of Mlu Cell Cycle Box (MCB); 7.3 Summary; 7.4 Further Reading 8 Automated Analysis, Integrated Analysis, and Systems Biology8.1 Integrated Analysis; 8.2 Systems Biology; 8.3 Further Reading; 9 Reverse Engineering of Regulatory Networks; 9.1 The Time-Series Approach; 9.2 The Steady-State Approach; 9.3 Limitations of Network Modeling; 9.4 Example 1: Steady-State Model; 9.5 Example 2: Steady-State Model on Bacillus Data; 9.6 Example 3: Linear Time-Series Model; 9.7 Further Reading; 10 Molecular Classifiers; 10.1 Feature Selection; 10.2 Validation; 10.3 Classification Schemes; 10.3.1 Nearest Neighbor; 10.3.2 Nearest Centroid; 10.3.3 Neural Networks 10.3.4 Support Vector Machine |
| Altri titoli varianti | Analysis of DNA microarray data |
| Record Nr. | UNINA-9910877020803321 |
|
Knudsen Steen
|
||
| Hoboken, N.J., : Wiley-Liss, c2004 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||