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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-9910841365003321 |
| Chichester, West Sussex ; ; Hoboken, : J. Wiley, 2009 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Bayesian analysis of gene expression data [[electronic resource] /] / edited by Bani Mallick, David Gold, and Veera Baladandayuthapani
| Bayesian analysis of gene expression data [[electronic resource] /] / edited by Bani Mallick, David Gold, and Veera Baladandayuthapani |
| Autore | Mallick Bani K. <1965-> |
| Pubbl/distr/stampa | Hoboken, N.J., : Wiley, 2009 |
| Descrizione fisica | 1 online resource (254 p.) |
| Disciplina |
572.8
572.86501519542 |
| Altri autori (Persone) |
MallickBani K. <1965->
GoldDavid <1970-> BaladandayuthapaniVeerabhadran <1976-> |
| Collana | Statistics in practice |
| Soggetto topico |
Gene expression - Statistical methods
Bayesian statistical decision theory |
| ISBN |
1-282-34942-2
9786612349423 0-470-74278-X 0-470-74281-X |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Bayesian Analysis of Gene Expression Data; Contents; Table of Notation; 1 Bioinformatics and Gene Expression Experiments; 1.1 Introduction; 1.2 About This Book; 2 Gene Expression Data: Basic Biology and Experiments; 2.1 Background Biology; 2.1.1 DNA Structures and Transcription; 2.2 Gene Expression Microarray Experiments; 2.2.1 Microarray Designs; 2.2.2 Work Flow; 2.2.3 Data Cleaning; 3 Bayesian Linear Models for Gene Expression; 3.1 Introduction; 3.2 Bayesian Analysis of a Linear Model; 3.2.1 Analysis via Conjugate Priors; 3.2.2 Bayesian Variable Selection; 3.2.3 Model Selection Priors
3.2.4 Priors on Regression Coefficients3.2.5 Sparsity Priors; 3.3 Bayesian Linear Models for Differential Expression; 3.3.1 Relevant Work; 3.4 Bayesian ANOVA for Gene Selection; 3.4.1 The Basic Bayesian ANOVA Model; 3.4.2 Differential Expression via Model Selection; 3.5 Robust ANOVA model with Mixtures of Singular Distributions; 3.6 Case Study; 3.7 Accounting for Nuisance Effects; 3.8 Summary and Further Reading; 4 Bayesian Multiple Testing and False Discovery Rate Analysis; 4.1 Introduction to Multiple Testing; 4.2 False Discovery Rate Analysis; 4.2.1 Theoretical Developments 4.2.2 FDR Analysis with Gene Expression Arrays4.3 Bayesian False Discovery Rate Analysis; 4.3.1 Theoretical Developments; 4.4 Bayesian Estimation of FDR; 4.5 FDR and Decision Theory; 4.6 FDR and bFDR Summary; 5 Bayesian Classification for Microarray Data; 5.1 Introduction; 5.2 Classification and Discriminant Rules; 5.3 Bayesian Discriminant Analysis; 5.4 Bayesian Regression Based Approaches to Classification; 5.4.1 Bayesian Analysis of Generalized Linear Models; 5.4.2 Link Functions; 5.4.3 GLM using Latent Processes; 5.4.4 Priors and Computation 5.4.5 Bayesian Probit Regression using Auxiliary Variables5.5 Bayesian Nonlinear Classification; 5.5.1 Classification using Interactions; 5.5.2 Classification using Kernel Methods; 5.6 Prediction and Model Choice; 5.7 Examples; 5.8 Discussion; 6 Bayesian Hypothesis Inference for Gene Classes; 6.1 Interpreting Microarray Results; 6.2 Gene Classes; 6.2.1 Enrichment Analysis; 6.3 Bayesian Enrichment Analysis; 6.4 Multivariate Gene Class Detection; 6.4.1 Extending the Bayesian ANOVA Model; 6.4.2 Bayesian Decomposition; 6.5 Summary; 7 Unsupervised Classification and Bayesian Clustering 7.1 Introduction to Bayesian Clustering for Gene Expression Data7.2 Hierarchical Clustering; 7.3 K-Means Clustering; 7.4 Model-Based Clustering; 7.5 Model-Based Agglomerative Hierarchical Clustering; 7.6 Bayesian Clustering; 7.7 Principal Components; 7.8 Mixture Modeling; 7.8.1 Label Switching; 7.9 Clustering Using Dirichlet Process Prior; 7.9.1 Infinite Mixture of Gaussian Distributions; 8 Bayesian Graphical Models; 8.1 Introduction; 8.2 Probabilistic Graphical Models; 8.3 Bayesian Networks; 8.4 Inference for Network Models; 8.4.1 Multinomial-Dirichlet Model; 8.4.2 Gaussian Model 8.4.3 Model Search |
| Record Nr. | UNINA-9910139785403321 |
Mallick Bani K. <1965->
|
||
| Hoboken, N.J., : Wiley, 2009 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Bayesian analysis of gene expression data [[electronic resource] /] / edited by Bani Mallick, David Gold, and Veera Baladandayuthapani
| Bayesian analysis of gene expression data [[electronic resource] /] / edited by Bani Mallick, David Gold, and Veera Baladandayuthapani |
| Autore | Mallick Bani K. <1965-> |
| Pubbl/distr/stampa | Hoboken, N.J., : Wiley, 2009 |
| Descrizione fisica | 1 online resource (254 p.) |
| Disciplina |
572.8
572.86501519542 |
| Altri autori (Persone) |
MallickBani K. <1965->
GoldDavid <1970-> BaladandayuthapaniVeerabhadran <1976-> |
| Collana | Statistics in practice |
| Soggetto topico |
Gene expression - Statistical methods
Bayesian statistical decision theory |
| ISBN |
1-282-34942-2
9786612349423 0-470-74278-X 0-470-74281-X |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Bayesian Analysis of Gene Expression Data; Contents; Table of Notation; 1 Bioinformatics and Gene Expression Experiments; 1.1 Introduction; 1.2 About This Book; 2 Gene Expression Data: Basic Biology and Experiments; 2.1 Background Biology; 2.1.1 DNA Structures and Transcription; 2.2 Gene Expression Microarray Experiments; 2.2.1 Microarray Designs; 2.2.2 Work Flow; 2.2.3 Data Cleaning; 3 Bayesian Linear Models for Gene Expression; 3.1 Introduction; 3.2 Bayesian Analysis of a Linear Model; 3.2.1 Analysis via Conjugate Priors; 3.2.2 Bayesian Variable Selection; 3.2.3 Model Selection Priors
3.2.4 Priors on Regression Coefficients3.2.5 Sparsity Priors; 3.3 Bayesian Linear Models for Differential Expression; 3.3.1 Relevant Work; 3.4 Bayesian ANOVA for Gene Selection; 3.4.1 The Basic Bayesian ANOVA Model; 3.4.2 Differential Expression via Model Selection; 3.5 Robust ANOVA model with Mixtures of Singular Distributions; 3.6 Case Study; 3.7 Accounting for Nuisance Effects; 3.8 Summary and Further Reading; 4 Bayesian Multiple Testing and False Discovery Rate Analysis; 4.1 Introduction to Multiple Testing; 4.2 False Discovery Rate Analysis; 4.2.1 Theoretical Developments 4.2.2 FDR Analysis with Gene Expression Arrays4.3 Bayesian False Discovery Rate Analysis; 4.3.1 Theoretical Developments; 4.4 Bayesian Estimation of FDR; 4.5 FDR and Decision Theory; 4.6 FDR and bFDR Summary; 5 Bayesian Classification for Microarray Data; 5.1 Introduction; 5.2 Classification and Discriminant Rules; 5.3 Bayesian Discriminant Analysis; 5.4 Bayesian Regression Based Approaches to Classification; 5.4.1 Bayesian Analysis of Generalized Linear Models; 5.4.2 Link Functions; 5.4.3 GLM using Latent Processes; 5.4.4 Priors and Computation 5.4.5 Bayesian Probit Regression using Auxiliary Variables5.5 Bayesian Nonlinear Classification; 5.5.1 Classification using Interactions; 5.5.2 Classification using Kernel Methods; 5.6 Prediction and Model Choice; 5.7 Examples; 5.8 Discussion; 6 Bayesian Hypothesis Inference for Gene Classes; 6.1 Interpreting Microarray Results; 6.2 Gene Classes; 6.2.1 Enrichment Analysis; 6.3 Bayesian Enrichment Analysis; 6.4 Multivariate Gene Class Detection; 6.4.1 Extending the Bayesian ANOVA Model; 6.4.2 Bayesian Decomposition; 6.5 Summary; 7 Unsupervised Classification and Bayesian Clustering 7.1 Introduction to Bayesian Clustering for Gene Expression Data7.2 Hierarchical Clustering; 7.3 K-Means Clustering; 7.4 Model-Based Clustering; 7.5 Model-Based Agglomerative Hierarchical Clustering; 7.6 Bayesian Clustering; 7.7 Principal Components; 7.8 Mixture Modeling; 7.8.1 Label Switching; 7.9 Clustering Using Dirichlet Process Prior; 7.9.1 Infinite Mixture of Gaussian Distributions; 8 Bayesian Graphical Models; 8.1 Introduction; 8.2 Probabilistic Graphical Models; 8.3 Bayesian Networks; 8.4 Inference for Network Models; 8.4.1 Multinomial-Dirichlet Model; 8.4.2 Gaussian Model 8.4.3 Model Search |
| Record Nr. | UNINA-9910830664603321 |
|
Mallick Bani K. <1965->
|
||
| Hoboken, N.J., : Wiley, 2009 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Bayesian analysis of gene expression data [[electronic resource] /] / edited by Bani Mallick, David Gold, and Veera Baladandayuthapani
| Bayesian analysis of gene expression data [[electronic resource] /] / edited by Bani Mallick, David Gold, and Veera Baladandayuthapani |
| Autore | Mallick Bani K. <1965-> |
| Pubbl/distr/stampa | Hoboken, N.J., : Wiley, 2009 |
| Descrizione fisica | 1 online resource (254 p.) |
| Disciplina |
572.8
572.86501519542 |
| Altri autori (Persone) |
MallickBani K. <1965->
GoldDavid <1970-> BaladandayuthapaniVeerabhadran <1976-> |
| Collana | Statistics in practice |
| Soggetto topico |
Gene expression - Statistical methods
Bayesian statistical decision theory |
| ISBN |
1-282-34942-2
9786612349423 0-470-74278-X 0-470-74281-X |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Bayesian Analysis of Gene Expression Data; Contents; Table of Notation; 1 Bioinformatics and Gene Expression Experiments; 1.1 Introduction; 1.2 About This Book; 2 Gene Expression Data: Basic Biology and Experiments; 2.1 Background Biology; 2.1.1 DNA Structures and Transcription; 2.2 Gene Expression Microarray Experiments; 2.2.1 Microarray Designs; 2.2.2 Work Flow; 2.2.3 Data Cleaning; 3 Bayesian Linear Models for Gene Expression; 3.1 Introduction; 3.2 Bayesian Analysis of a Linear Model; 3.2.1 Analysis via Conjugate Priors; 3.2.2 Bayesian Variable Selection; 3.2.3 Model Selection Priors
3.2.4 Priors on Regression Coefficients3.2.5 Sparsity Priors; 3.3 Bayesian Linear Models for Differential Expression; 3.3.1 Relevant Work; 3.4 Bayesian ANOVA for Gene Selection; 3.4.1 The Basic Bayesian ANOVA Model; 3.4.2 Differential Expression via Model Selection; 3.5 Robust ANOVA model with Mixtures of Singular Distributions; 3.6 Case Study; 3.7 Accounting for Nuisance Effects; 3.8 Summary and Further Reading; 4 Bayesian Multiple Testing and False Discovery Rate Analysis; 4.1 Introduction to Multiple Testing; 4.2 False Discovery Rate Analysis; 4.2.1 Theoretical Developments 4.2.2 FDR Analysis with Gene Expression Arrays4.3 Bayesian False Discovery Rate Analysis; 4.3.1 Theoretical Developments; 4.4 Bayesian Estimation of FDR; 4.5 FDR and Decision Theory; 4.6 FDR and bFDR Summary; 5 Bayesian Classification for Microarray Data; 5.1 Introduction; 5.2 Classification and Discriminant Rules; 5.3 Bayesian Discriminant Analysis; 5.4 Bayesian Regression Based Approaches to Classification; 5.4.1 Bayesian Analysis of Generalized Linear Models; 5.4.2 Link Functions; 5.4.3 GLM using Latent Processes; 5.4.4 Priors and Computation 5.4.5 Bayesian Probit Regression using Auxiliary Variables5.5 Bayesian Nonlinear Classification; 5.5.1 Classification using Interactions; 5.5.2 Classification using Kernel Methods; 5.6 Prediction and Model Choice; 5.7 Examples; 5.8 Discussion; 6 Bayesian Hypothesis Inference for Gene Classes; 6.1 Interpreting Microarray Results; 6.2 Gene Classes; 6.2.1 Enrichment Analysis; 6.3 Bayesian Enrichment Analysis; 6.4 Multivariate Gene Class Detection; 6.4.1 Extending the Bayesian ANOVA Model; 6.4.2 Bayesian Decomposition; 6.5 Summary; 7 Unsupervised Classification and Bayesian Clustering 7.1 Introduction to Bayesian Clustering for Gene Expression Data7.2 Hierarchical Clustering; 7.3 K-Means Clustering; 7.4 Model-Based Clustering; 7.5 Model-Based Agglomerative Hierarchical Clustering; 7.6 Bayesian Clustering; 7.7 Principal Components; 7.8 Mixture Modeling; 7.8.1 Label Switching; 7.9 Clustering Using Dirichlet Process Prior; 7.9.1 Infinite Mixture of Gaussian Distributions; 8 Bayesian Graphical Models; 8.1 Introduction; 8.2 Probabilistic Graphical Models; 8.3 Bayesian Networks; 8.4 Inference for Network Models; 8.4.1 Multinomial-Dirichlet Model; 8.4.2 Gaussian Model 8.4.3 Model Search |
| Record Nr. | UNINA-9910841086203321 |
|
Mallick Bani K. <1965->
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||
| Hoboken, N.J., : Wiley, 2009 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Biochemical Analysis Tools : Methods for Bio-Molecules Studies / / edited by Oana-Maria Boldura, Cornel Baltă, Nasser Sayed Awwad
| Biochemical Analysis Tools : Methods for Bio-Molecules Studies / / edited by Oana-Maria Boldura, Cornel Baltă, Nasser Sayed Awwad |
| Pubbl/distr/stampa | London : , : IntechOpen, , 2020 |
| Descrizione fisica | 1 online resource (206 pages) : illustrations |
| Disciplina | 572.8 |
| Soggetto topico |
Molecular biology - Methodology
Nucleic acids - Analysis Analytical biochemistry |
| ISBN | 1-78984-857-1 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Altri titoli varianti | Biochemical Analysis Tools |
| Record Nr. | UNINA-9910409734003321 |
| London : , : IntechOpen, , 2020 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Biochemical genetics
| Biochemical genetics |
| Pubbl/distr/stampa | Dordrecht, : Kluwer Academic Publishers, 1967- |
| Descrizione fisica | 1 online resource |
| Disciplina | 572.8 |
| Soggetto topico |
Biochemical genetics
Biochemistry Genetics biochemistry genetics molecular biology Génétique biochimique Biochimie |
| Soggetto genere / forma | Periodicals. |
| ISSN | 1573-4927 |
| Formato | Materiale a stampa |
| Livello bibliografico | Periodico |
| Lingua di pubblicazione | eng |
| Record Nr. | UNINA-9910140757503321 |
| Dordrecht, : Kluwer Academic Publishers, 1967- | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Biochemical genetics
| Biochemical genetics |
| Pubbl/distr/stampa | Dordrecht, : Kluwer Academic Publishers, 1967- |
| Descrizione fisica | 1 online resource |
| Disciplina | 572.8 |
| Soggetto topico |
Biochemical genetics
Biochemistry Genetics biochemistry genetics molecular biology Génétique biochimique Biochimie |
| Soggetto genere / forma | Periodicals. |
| ISSN | 1573-4927 |
| Formato | Materiale a stampa |
| Livello bibliografico | Periodico |
| Lingua di pubblicazione | eng |
| Record Nr. | UNISA-996214108503316 |
| Dordrecht, : Kluwer Academic Publishers, 1967- | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. di Salerno | ||
| ||
Biochemistry and molecular biology / William H. Elliott and Daphne C. Elliott
| Biochemistry and molecular biology / William H. Elliott and Daphne C. Elliott |
| Autore | Elliott, William H. |
| Pubbl/distr/stampa | Oxford, : Oxford University Press, 1997 |
| Descrizione fisica | XXV, 437 p. ; 26 cm |
| Disciplina | 572.8 |
| Altri autori (Persone) | Elliott, Daphne C. |
| Soggetto non controllato |
Genetica biochimica
Biologia molecolare |
| ISBN | 0-19-857793-1 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | ita |
| Record Nr. | UNINA-990001805000403321 |
|
Elliott, William H.
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| Oxford, : Oxford University Press, 1997 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Biochemistry and molecular biology education
| Biochemistry and molecular biology education |
| Pubbl/distr/stampa | Kidlington, : Elsevier, 2000- |
| Descrizione fisica | volumi : ill. ; 28 cm |
| Disciplina |
572(Biochimica. Citochimica. Istochimica)
572.8(Biologia molecolare. Genetica molecolare. Genetica fisiologica. Acidi nucleici) |
| Formato | Materiale a stampa |
| Livello bibliografico | Periodico |
| Lingua di pubblicazione | eng |
| Record Nr. | UNICAMPANIA-VAN0264726 |
| Kidlington, : Elsevier, 2000- | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Vanvitelli | ||
| ||
Biochemistry and molecular biology education
| Biochemistry and molecular biology education |
| Pubbl/distr/stampa | Kidlington, : Wiley, 2000- |
| Descrizione fisica | volumi : ill. ; 28 cm |
| Disciplina |
572(Biochimica. Citochimica. Istochimica)
572.8(Biologia molecolare. Genetica molecolare. Genetica fisiologica. Acidi nucleici) |
| ISSN | 1470-8175 |
| Formato | Materiale a stampa |
| Livello bibliografico | Periodico |
| Lingua di pubblicazione | eng |
| Record Nr. | UNICAMPANIA-VAN0044889 |
| Kidlington, : Wiley, 2000- | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Vanvitelli | ||
| ||
