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Analysis of microarray data : a network-based approach / / edited by Frank Emmert-Streib and Matthias Dehmer
| Analysis of microarray data : a network-based approach / / edited by Frank Emmert-Streib and Matthias Dehmer |
| Pubbl/distr/stampa | Weinheim, [Germany] : , : Wiley-VCH Verlag GmbH & Co. KGaA, , 2008 |
| Descrizione fisica | 1 online resource (440 p.) |
| Disciplina | 572.8636 |
| Soggetto topico | DNA microarrays |
| Soggetto genere / forma | Electronic books. |
| ISBN |
1-281-94703-2
9786611947033 3-527-62281-0 3-527-62282-9 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Analysis of Microarray Data; Contents; Preface; List of Contributors; 1 Introduction to DNA Microarrays; 1.1 Introduction; 1.1.1 The Genome is an Information Scaffold; 1.1.2 Gene Expression is Detected by Hybridization; 1.1.2.1 Hybridization is Used to Measure Gene Expression; 1.1.2.2 Microarrays Provide a New Twist to an Old Technique; 1.2 Types of Arrays; 1.2.1 Spotted Microarrays; 1.2.2 Affymetrix GeneChips; 1.2.2.1 Other In Situ Synthesis Platforms; 1.2.2.2 Uses of Microarrays; 1.3 Array Content; 1.3.1 ESTs Are the First View; 1.3.1.1 Probe Design; 1.4 Normalization and Scaling
1.4.1 Be Unbiased, Be Complete1.4.2 Sequence Counts; References; 2 Comparative Analysis of Clustering Methods for Microarray Data; 2.1 Introduction; 2.2 Measuring Distance Between Genes or Clusters; 2.3 Network Models; 2.3.1 Boolean Network; 2.3.2 Coexpression Network; 2.3.3 Bayesian Network; 2.3.4 Co-Occurrence Network; 2.4 Network Constrained Clustering Method; 2.4.1 Extract the Giant Connected Component; 2.4.2 Compute "Network Constrained Distance Matrix"; 2.5 Network Constrained Clustering Results; 2.5.1 Yeast Galactose Metabolism Pathway; 2.5.2 Retinal Gene Expression Data 2.5.3 Mouse Segmentation Clock Data2.6 Discussion and Conclusion; References; 3 Finding Verified Edges in Genetic/Gene Networks: Bilayer Verification for Network Recovery in the Presence of Hidden Confounders; 3.1 Introduction: Gene and Genetic Networks; 3.2 Background and Prior Theory; 3.2.1 Motivation; 3.2.2 Bayesian Networks Theory; 3.2.2.1 d-Separation at Colliders; 3.2.2.2 Placing Genetic Tests Within the Bayesian Network Framework; 3.2.3 Learning Network Structure from Observed Conditional Independencies; 3.2.4 Prior Work: The PC Algorithm; 3.2.4.1 PC Algorithm 3.5 Results and Further Application3.5.1 Estimating α False-Positive Rates for the v-Structure Test; 3.5.2 Learning an Aortic Lesion Network; 3.5.3 Further Utilizing Networks: Assigning Functional Roles to Genes; 3.5.4 Future Work; References; 4 Computational Inference of Biological Causal Networks - Analysis of Therapeutic Compound Effects; 4.1 Introduction; 4.2 Basic Theory of Bayesian Networks; 4.2.1 Bayesian Scoring Metrics; 4.2.2 Heuristic Search Methods; 4.2.3 Inference Score; 4.3 Methods; 4.3.1 Experimental Design; 4.3.2 Tissue Contamination; 4.3.3 Gene List Prefiltering 4.3.4 Outlier Removal |
| Record Nr. | UNINA-9910144107303321 |
| Weinheim, [Germany] : , : Wiley-VCH Verlag GmbH & Co. KGaA, , 2008 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Analysis of microarray data : a network-based approach / / edited by Frank Emmert-Streib and Matthias Dehmer
| Analysis of microarray data : a network-based approach / / edited by Frank Emmert-Streib and Matthias Dehmer |
| Pubbl/distr/stampa | Weinheim, [Germany] : , : Wiley-VCH Verlag GmbH & Co. KGaA, , 2008 |
| Descrizione fisica | 1 online resource (440 p.) |
| Disciplina | 572.8636 |
| Soggetto topico | DNA microarrays |
| ISBN |
1-281-94703-2
9786611947033 3-527-62281-0 3-527-62282-9 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Analysis of Microarray Data; Contents; Preface; List of Contributors; 1 Introduction to DNA Microarrays; 1.1 Introduction; 1.1.1 The Genome is an Information Scaffold; 1.1.2 Gene Expression is Detected by Hybridization; 1.1.2.1 Hybridization is Used to Measure Gene Expression; 1.1.2.2 Microarrays Provide a New Twist to an Old Technique; 1.2 Types of Arrays; 1.2.1 Spotted Microarrays; 1.2.2 Affymetrix GeneChips; 1.2.2.1 Other In Situ Synthesis Platforms; 1.2.2.2 Uses of Microarrays; 1.3 Array Content; 1.3.1 ESTs Are the First View; 1.3.1.1 Probe Design; 1.4 Normalization and Scaling
1.4.1 Be Unbiased, Be Complete1.4.2 Sequence Counts; References; 2 Comparative Analysis of Clustering Methods for Microarray Data; 2.1 Introduction; 2.2 Measuring Distance Between Genes or Clusters; 2.3 Network Models; 2.3.1 Boolean Network; 2.3.2 Coexpression Network; 2.3.3 Bayesian Network; 2.3.4 Co-Occurrence Network; 2.4 Network Constrained Clustering Method; 2.4.1 Extract the Giant Connected Component; 2.4.2 Compute "Network Constrained Distance Matrix"; 2.5 Network Constrained Clustering Results; 2.5.1 Yeast Galactose Metabolism Pathway; 2.5.2 Retinal Gene Expression Data 2.5.3 Mouse Segmentation Clock Data2.6 Discussion and Conclusion; References; 3 Finding Verified Edges in Genetic/Gene Networks: Bilayer Verification for Network Recovery in the Presence of Hidden Confounders; 3.1 Introduction: Gene and Genetic Networks; 3.2 Background and Prior Theory; 3.2.1 Motivation; 3.2.2 Bayesian Networks Theory; 3.2.2.1 d-Separation at Colliders; 3.2.2.2 Placing Genetic Tests Within the Bayesian Network Framework; 3.2.3 Learning Network Structure from Observed Conditional Independencies; 3.2.4 Prior Work: The PC Algorithm; 3.2.4.1 PC Algorithm 3.5 Results and Further Application3.5.1 Estimating α False-Positive Rates for the v-Structure Test; 3.5.2 Learning an Aortic Lesion Network; 3.5.3 Further Utilizing Networks: Assigning Functional Roles to Genes; 3.5.4 Future Work; References; 4 Computational Inference of Biological Causal Networks - Analysis of Therapeutic Compound Effects; 4.1 Introduction; 4.2 Basic Theory of Bayesian Networks; 4.2.1 Bayesian Scoring Metrics; 4.2.2 Heuristic Search Methods; 4.2.3 Inference Score; 4.3 Methods; 4.3.1 Experimental Design; 4.3.2 Tissue Contamination; 4.3.3 Gene List Prefiltering 4.3.4 Outlier Removal |
| Record Nr. | UNINA-9910830082603321 |
| Weinheim, [Germany] : , : Wiley-VCH Verlag GmbH & Co. KGaA, , 2008 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Applying genomic and proteomic microarray technology in drug discovery / / Robert S. Matson
| Applying genomic and proteomic microarray technology in drug discovery / / Robert S. Matson |
| Autore | Matson Robert S. |
| Edizione | [2nd ed.] |
| Pubbl/distr/stampa | Boca Raton : , : Taylor & Francis, , 2013 |
| Descrizione fisica | 1 online resource (313 p.) |
| Disciplina | 615.1/9 |
| Soggetto topico |
High throughput screening (Drug development)
DNA microarrays Protein microarrays Pharmacogenomics Proteomics |
| Soggetto genere / forma | Electronic books. |
| ISBN |
0-429-10783-8
1-4398-5564-1 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Omics & microarrays revisited -- The commercial microarray -- Supports & surface chemistries -- The arraying process -- Gene expression microarray-based applications -- Protein microarray applications -- Multiplex assays. |
| Record Nr. | UNINA-9910462913103321 |
Matson Robert S.
|
||
| Boca Raton : , : Taylor & Francis, , 2013 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Applying genomic and proteomic microarray technology in drug discovery / / Robert S. Matson
| Applying genomic and proteomic microarray technology in drug discovery / / Robert S. Matson |
| Autore | Matson Robert S. |
| Edizione | [2nd ed.] |
| Pubbl/distr/stampa | Boca Raton : , : Taylor & Francis, , 2013 |
| Descrizione fisica | 1 online resource (313 p.) |
| Disciplina | 615.1/9 |
| Soggetto topico |
High throughput screening (Drug development)
DNA microarrays Protein microarrays Pharmacogenomics Proteomics |
| ISBN |
0-429-10783-8
1-4398-5564-1 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Omics & microarrays revisited -- The commercial microarray -- Supports & surface chemistries -- The arraying process -- Gene expression microarray-based applications -- Protein microarray applications -- Multiplex assays. |
| Record Nr. | UNINA-9910786247103321 |
|
Matson Robert S.
|
||
| Boca Raton : , : Taylor & Francis, , 2013 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Applying genomic and proteomic microarray technology in drug discovery / / Robert S. Matson
| Applying genomic and proteomic microarray technology in drug discovery / / Robert S. Matson |
| Autore | Matson Robert S. |
| Edizione | [2nd ed.] |
| Pubbl/distr/stampa | Boca Raton : , : Taylor & Francis, , 2013 |
| Descrizione fisica | 1 online resource (313 p.) |
| Disciplina | 615.1/9 |
| Soggetto topico |
High throughput screening (Drug development)
DNA microarrays Protein microarrays Pharmacogenomics Proteomics |
| ISBN |
0-429-10783-8
1-4398-5564-1 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Omics & microarrays revisited -- The commercial microarray -- Supports & surface chemistries -- The arraying process -- Gene expression microarray-based applications -- Protein microarray applications -- Multiplex assays. |
| Record Nr. | UNINA-9910800038603321 |
|
Matson Robert S.
|
||
| Boca Raton : , : Taylor & Francis, , 2013 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Applying genomic and proteomic microarray technology in drug discovery / / Robert S. Matson
| Applying genomic and proteomic microarray technology in drug discovery / / Robert S. Matson |
| Autore | Matson Robert S. |
| Edizione | [2nd ed.] |
| Pubbl/distr/stampa | Boca Raton, : Taylor & Francis, 2013 |
| Descrizione fisica | 1 online resource (313 p.) |
| Disciplina | 615.1/9 |
| Soggetto topico |
High throughput screening (Drug development)
DNA microarrays Protein microarrays Pharmacogenomics Proteomics |
| ISBN |
1-04-006064-1
0-429-10783-8 1-4398-5564-1 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Omics & microarrays revisited -- The commercial microarray -- Supports & surface chemistries -- The arraying process -- Gene expression microarray-based applications -- Protein microarray applications -- Multiplex assays. |
| Record Nr. | UNINA-9910822584903321 |
|
Matson Robert S.
|
||
| Boca Raton, : Taylor & Francis, 2013 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Avian intestinal microarray analysis ... annual report
| Avian intestinal microarray analysis ... annual report |
| Pubbl/distr/stampa | Washington, D.C., : U.S. Dept. of Agriculture, Agricultural Research Service |
| Descrizione fisica | : HTML files |
| Disciplina | 571 |
| Soggetto topico |
Poultry - Pathogens
DNA microarrays Intestinal mucosa - Diseases Poultry - Immunology - Genetic aspects |
| Soggetto genere / forma | Periodicals. |
| ISSN | 1948-3716 |
| Formato | Materiale a stampa |
| Livello bibliografico | Periodico |
| Lingua di pubblicazione | eng |
| Record Nr. | UNINA-9910698668503321 |
| Washington, D.C., : U.S. Dept. of Agriculture, Agricultural Research Service | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Batch effects and noise in microarray experiments, sources, and solutions [[electronic resource] /] / edited by Andreas Scherer
| Batch effects and noise in microarray experiments, sources, and solutions [[electronic resource] /] / edited by Andreas Scherer |
| Pubbl/distr/stampa | Chichester, West Sussex ; ; Hoboken, : J. Wiley, 2009 |
| Descrizione fisica | 1 online resource (282 p.) |
| Disciplina |
572.8
572.8636 611.01816 |
| Altri autori (Persone) | SchererAndreas <1966-> |
| Collana | Wiley Series in Probability and Statistics |
| Soggetto topico |
DNA microarrays
DNA microarrays - Experiments |
| Soggetto genere / forma | Electronic books. |
| ISBN |
1-282-37950-X
9786612379505 0-470-68598-0 0-470-68599-9 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Batch Effects and Noise in Microarray Experiments; Contents; List of Contributors; Foreword; Preface; 1 Variation, Variability, Batches and Bias in Microarray Experiments: An Introduction; 2 Microarray Platforms and Aspects of Experimental Variation; 2.1 Introduction; 2.2 Microarray Platforms; 2.2.1 Affymetrix; 2.2.2 Agilent; 2.2.3 Illumina; 2.2.4 Nimblegen; 2.2.5 Spotted Microarrays; 2.3 Experimental Considerations; 2.3.1 Experimental Design; 2.3.2 Sample and RNA Extraction; 2.3.3 Amplification; 2.3.4 Labeling; 2.3.5 Hybridization; 2.3.6 Washing; 2.3.7 Scanning
2.3.8 Image Analysis and Data Extraction2.3.9 Clinical Diagnosis; 2.3.10 Interpretation of the Data; 2.4 Conclusions; 3 Experimental Design; 3.1 Introduction; 3.2 Principles of Experimental Design; 3.2.1 Definitions; 3.2.2 Technical Variation; 3.2.3 Biological Variation; 3.2.4 Systematic Variation; 3.2.5 Population, Random Sample, Experimental and Observational Units; 3.2.6 Experimental Factors; 3.2.7 Statistical Errors; 3.3 Measures to Increase Precision and Accuracy; 3.3.1 Randomization; 3.3.2 Blocking; 3.3.3 Replication; 3.3.4 Further Measures to Optimize Study Design 3.4 Systematic Errors in Microarray Studies3.4.1 Selection Bias; 3.4.2 Observational Bias; 3.4.3 Bias at Specimen/Tissue Collection; 3.4.4 Bias at mRNA Extraction and Hybridization; 3.5 Conclusion; 4 Batches and Blocks, Sample Pools and Subsamples in the Design and Analysis of Gene Expression Studies; 4.1 Introduction; 4.1.1 Batch Effects; 4.2 A Statistical Linear Mixed Effects Model for Microarray Experiments; 4.2.1 Using the Linear Model for Design; 4.2.2 Examples of Design Guided by the Linear Model; 4.3 Blocks and Batches; 4.3.1 Complete Block Designs; 4.3.2 Incomplete Block Designs 4.3.3 Multiple Batch Effects4.4 Reducing Batch Effects by Normalization and Statistical Adjustment; 4.4.1 Between and Within Batch Normalization with Multi-array Methods; 4.4.2 Statistical Adjustment; 4.5 Sample Pooling and Sample Splitting; 4.5.1 Sample Pooling; 4.5.2 Sample Splitting: Technical Replicates; 4.6 Pilot Experiments; 4.7 Conclusions; Acknowledgements; 5 Aspects of Technical Bias; 5.1 Introduction; 5.2 Observational Studies; 5.2.1 Same Protocol, Different Times of Processing; 5.2.2 Same Protocol, Different Sites (Study 1); 5.2.3 Same Protocol, Different Sites (Study 2) 5.2.4 Batch Effect Characteristics at the Probe Level5.3 Conclusion; 6 Bioinformatic Strategies for cDNA-Microarray Data Processing; 6.1 Introduction; 6.1.1 Spike-in Experiments; 6.1.2 Key Measures - Sensitivity and Bias; 6.1.3 The IC Curve and MA Plot; 6.2 Pre-processing; 6.2.1 Scanning Procedures; 6.2.2 Background Correction; 6.2.3 Saturation; 6.2.4 Normalization; 6.2.5 Filtering; 6.3 Downstream Analysis; 6.3.1 Gene Selection; 6.3.2 Cluster Analysis; 6.4 Conclusion; 7 Batch Effect Estimation of Microarray Platforms with Analysis of Variance; 7.1 Introduction 7.1.1 Microarray Gene Expression Data |
| Record Nr. | UNINA-9910139958503321 |
| Chichester, West Sussex ; ; Hoboken, : J. Wiley, 2009 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Batch effects and noise in microarray experiments, sources, and solutions [[electronic resource] /] / edited by Andreas Scherer
| Batch effects and noise in microarray experiments, sources, and solutions [[electronic resource] /] / edited by Andreas Scherer |
| Pubbl/distr/stampa | Chichester, West Sussex ; ; Hoboken, : J. Wiley, 2009 |
| Descrizione fisica | 1 online resource (282 p.) |
| Disciplina |
572.8
572.8636 611.01816 |
| Altri autori (Persone) | SchererAndreas <1966-> |
| Collana | Wiley Series in Probability and Statistics |
| Soggetto topico |
DNA microarrays
DNA microarrays - Experiments |
| ISBN |
1-282-37950-X
9786612379505 0-470-68598-0 0-470-68599-9 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Batch Effects and Noise in Microarray Experiments; Contents; List of Contributors; Foreword; Preface; 1 Variation, Variability, Batches and Bias in Microarray Experiments: An Introduction; 2 Microarray Platforms and Aspects of Experimental Variation; 2.1 Introduction; 2.2 Microarray Platforms; 2.2.1 Affymetrix; 2.2.2 Agilent; 2.2.3 Illumina; 2.2.4 Nimblegen; 2.2.5 Spotted Microarrays; 2.3 Experimental Considerations; 2.3.1 Experimental Design; 2.3.2 Sample and RNA Extraction; 2.3.3 Amplification; 2.3.4 Labeling; 2.3.5 Hybridization; 2.3.6 Washing; 2.3.7 Scanning
2.3.8 Image Analysis and Data Extraction2.3.9 Clinical Diagnosis; 2.3.10 Interpretation of the Data; 2.4 Conclusions; 3 Experimental Design; 3.1 Introduction; 3.2 Principles of Experimental Design; 3.2.1 Definitions; 3.2.2 Technical Variation; 3.2.3 Biological Variation; 3.2.4 Systematic Variation; 3.2.5 Population, Random Sample, Experimental and Observational Units; 3.2.6 Experimental Factors; 3.2.7 Statistical Errors; 3.3 Measures to Increase Precision and Accuracy; 3.3.1 Randomization; 3.3.2 Blocking; 3.3.3 Replication; 3.3.4 Further Measures to Optimize Study Design 3.4 Systematic Errors in Microarray Studies3.4.1 Selection Bias; 3.4.2 Observational Bias; 3.4.3 Bias at Specimen/Tissue Collection; 3.4.4 Bias at mRNA Extraction and Hybridization; 3.5 Conclusion; 4 Batches and Blocks, Sample Pools and Subsamples in the Design and Analysis of Gene Expression Studies; 4.1 Introduction; 4.1.1 Batch Effects; 4.2 A Statistical Linear Mixed Effects Model for Microarray Experiments; 4.2.1 Using the Linear Model for Design; 4.2.2 Examples of Design Guided by the Linear Model; 4.3 Blocks and Batches; 4.3.1 Complete Block Designs; 4.3.2 Incomplete Block Designs 4.3.3 Multiple Batch Effects4.4 Reducing Batch Effects by Normalization and Statistical Adjustment; 4.4.1 Between and Within Batch Normalization with Multi-array Methods; 4.4.2 Statistical Adjustment; 4.5 Sample Pooling and Sample Splitting; 4.5.1 Sample Pooling; 4.5.2 Sample Splitting: Technical Replicates; 4.6 Pilot Experiments; 4.7 Conclusions; Acknowledgements; 5 Aspects of Technical Bias; 5.1 Introduction; 5.2 Observational Studies; 5.2.1 Same Protocol, Different Times of Processing; 5.2.2 Same Protocol, Different Sites (Study 1); 5.2.3 Same Protocol, Different Sites (Study 2) 5.2.4 Batch Effect Characteristics at the Probe Level5.3 Conclusion; 6 Bioinformatic Strategies for cDNA-Microarray Data Processing; 6.1 Introduction; 6.1.1 Spike-in Experiments; 6.1.2 Key Measures - Sensitivity and Bias; 6.1.3 The IC Curve and MA Plot; 6.2 Pre-processing; 6.2.1 Scanning Procedures; 6.2.2 Background Correction; 6.2.3 Saturation; 6.2.4 Normalization; 6.2.5 Filtering; 6.3 Downstream Analysis; 6.3.1 Gene Selection; 6.3.2 Cluster Analysis; 6.4 Conclusion; 7 Batch Effect Estimation of Microarray Platforms with Analysis of Variance; 7.1 Introduction 7.1.1 Microarray Gene Expression Data |
| Record Nr. | UNINA-9910831169203321 |
| Chichester, West Sussex ; ; Hoboken, : J. Wiley, 2009 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Batch effects and noise in microarray experiments, sources, and solutions / / edited by Andreas Scherer
| Batch effects and noise in microarray experiments, sources, and solutions / / edited by Andreas Scherer |
| Pubbl/distr/stampa | Chichester, West Sussex ; ; Hoboken, : J. Wiley, 2009 |
| Descrizione fisica | 1 online resource (282 p.) |
| Disciplina | 572.8/636 |
| Altri autori (Persone) | SchererAndreas <1966-> |
| Collana | Wiley Series in Probability and Statistics |
| Soggetto topico |
DNA microarrays
DNA microarrays - Experiments |
| ISBN |
1-282-37950-X
9786612379505 0-470-68598-0 0-470-68599-9 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Batch Effects and Noise in Microarray Experiments; Contents; List of Contributors; Foreword; Preface; 1 Variation, Variability, Batches and Bias in Microarray Experiments: An Introduction; 2 Microarray Platforms and Aspects of Experimental Variation; 2.1 Introduction; 2.2 Microarray Platforms; 2.2.1 Affymetrix; 2.2.2 Agilent; 2.2.3 Illumina; 2.2.4 Nimblegen; 2.2.5 Spotted Microarrays; 2.3 Experimental Considerations; 2.3.1 Experimental Design; 2.3.2 Sample and RNA Extraction; 2.3.3 Amplification; 2.3.4 Labeling; 2.3.5 Hybridization; 2.3.6 Washing; 2.3.7 Scanning
2.3.8 Image Analysis and Data Extraction2.3.9 Clinical Diagnosis; 2.3.10 Interpretation of the Data; 2.4 Conclusions; 3 Experimental Design; 3.1 Introduction; 3.2 Principles of Experimental Design; 3.2.1 Definitions; 3.2.2 Technical Variation; 3.2.3 Biological Variation; 3.2.4 Systematic Variation; 3.2.5 Population, Random Sample, Experimental and Observational Units; 3.2.6 Experimental Factors; 3.2.7 Statistical Errors; 3.3 Measures to Increase Precision and Accuracy; 3.3.1 Randomization; 3.3.2 Blocking; 3.3.3 Replication; 3.3.4 Further Measures to Optimize Study Design 3.4 Systematic Errors in Microarray Studies3.4.1 Selection Bias; 3.4.2 Observational Bias; 3.4.3 Bias at Specimen/Tissue Collection; 3.4.4 Bias at mRNA Extraction and Hybridization; 3.5 Conclusion; 4 Batches and Blocks, Sample Pools and Subsamples in the Design and Analysis of Gene Expression Studies; 4.1 Introduction; 4.1.1 Batch Effects; 4.2 A Statistical Linear Mixed Effects Model for Microarray Experiments; 4.2.1 Using the Linear Model for Design; 4.2.2 Examples of Design Guided by the Linear Model; 4.3 Blocks and Batches; 4.3.1 Complete Block Designs; 4.3.2 Incomplete Block Designs 4.3.3 Multiple Batch Effects4.4 Reducing Batch Effects by Normalization and Statistical Adjustment; 4.4.1 Between and Within Batch Normalization with Multi-array Methods; 4.4.2 Statistical Adjustment; 4.5 Sample Pooling and Sample Splitting; 4.5.1 Sample Pooling; 4.5.2 Sample Splitting: Technical Replicates; 4.6 Pilot Experiments; 4.7 Conclusions; Acknowledgements; 5 Aspects of Technical Bias; 5.1 Introduction; 5.2 Observational Studies; 5.2.1 Same Protocol, Different Times of Processing; 5.2.2 Same Protocol, Different Sites (Study 1); 5.2.3 Same Protocol, Different Sites (Study 2) 5.2.4 Batch Effect Characteristics at the Probe Level5.3 Conclusion; 6 Bioinformatic Strategies for cDNA-Microarray Data Processing; 6.1 Introduction; 6.1.1 Spike-in Experiments; 6.1.2 Key Measures - Sensitivity and Bias; 6.1.3 The IC Curve and MA Plot; 6.2 Pre-processing; 6.2.1 Scanning Procedures; 6.2.2 Background Correction; 6.2.3 Saturation; 6.2.4 Normalization; 6.2.5 Filtering; 6.3 Downstream Analysis; 6.3.1 Gene Selection; 6.3.2 Cluster Analysis; 6.4 Conclusion; 7 Batch Effect Estimation of Microarray Platforms with Analysis of Variance; 7.1 Introduction 7.1.1 Microarray Gene Expression Data |
| Record Nr. | UNINA-9910877873803321 |
| Chichester, West Sussex ; ; Hoboken, : J. Wiley, 2009 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Soggetto topico
-
DNA microarrays
(47)
- Gene expression (10)
- Pharmacogenomics (9)
- Proteomics (9)
- Protein microarrays (8)