爱学术-智能检索

Batch Effects and Noise in Microarray Experiments -- Sources and Solutions

微阵列实验中的批量效应和噪声

ISBN：9780470741382，出版年：2009，中图分类号：Q3 被引 154次

List of Contributors. Foreword. Preface. 1 Variation, Variability, Batches and Bias in Microarray Experiments: An Introduction ( Andreas Scherer). 2 Microarray Platforms and Aspects of Experimental Variation ( John A Coller Jr). 2.1 Introduction. 2.2 Microarray Platforms. 2.3 Experimental Considerations. 2.4 Conclusions. 3 Experimental Design ( Peter Grass). 3.1 Introduction. 3.2 Principles of Experimental Design. 3.3 Measures to Increase Precision and Accuracy. 3.4 Systematic Errors in Microarray Studies. 3.5 Conclusion. 4 Batches and Blocks, Sample Pools and Subsamples in the Design and Analysis of Gene Expression Studies ( Naomi Altman). 4.1 Introduction. 4.2 A Statistical Linear Mixed Effects Model for Microarray Experiments. 4.3 Blocks and Batches. 4.4 Reducing Batch Effects by Normalization and Statistical Adjustment. 4.5 Sample Pooling and Sample Splitting. 4.6 Pilot Experiments. 4.7 Conclusions. Acknowledgements. 5 Aspects of Technical Bias ( Martin Schumacher, Frank Staedtler, Wendell D Jones, and Andreas Scherer). 5.1 Introduction. 5.2 Observational Studies. 5.3 Conclusion. 6 Bioinformatic Strategies for cDNA-Microarray Data Processing ( Jessica Fahlen, Mattias Landfors, Eva Freyhult, Max Bylesjo, Johan Trygg, Torgeir R Hvidsten, and Patrik Ryden). 6.1 Introduction. 6.2 Pre-processing. 6.3 Downstream Analysis. 6.4 Conclusion. 7 Batch Effect Estimation of Microarray Platforms with Analysis of Variance ( Nysia I George and James J Chen). 7.1 Introduction. 7.2 Variance Component Analysis across Microarray Platforms. 7.3 Methodology. 7.4 Application: The MAQC Project. 7.5 Discussion and Conclusion. Acknowledgements. 8 Variance due to Smooth Bias in Rat Liver and Kidney Baseline Gene Expression in a Large Multi-laboratory Data Set ( Michael J Boedigheimer, Jeff W Chou, J Christopher Corton, Jennifer Fostel, Raegan O'Lone, P Scott Pine, John Quackenbush, Karol L Thompson, and Russell D Wolfinger). 8.1 Introduction. 8.2 Methodology. 8.3 Results. 8.4 Discussion. Acknowledgements. 9 Microarray Gene Expression: The Effects of Varying Certain Measurement Conditions ( Walter Liggett, Jean Lozach, Anne Bergstrom Lucas, Ron L Peterson, Marc L Salit, Danielle Thierry-Mieg, Jean Thierry-Mieg, and Russell D Wolfinger). 9.1 Introduction. 9.2 Input Mass Effect on the Amount of Normalization Applied. 9.3 Probe-by-Probe Modeling of the Input Mass Effect. 9.4 Further Evidence of Batch Effects. 9.5 Conclusions. 10 Adjusting Batch Effects in Microarray Experiments with Small Sample Size Using Empirical Bayes Methods ( W Evan Johnson and Cheng Li). 10.1 Introduction. 10.2 Existing Methods for Adjusting Batch Effect. 10.3 Empirical Bayes Method for Adjusting Batch Effect. 10.4 Data Examples, Results and Robustness of the Empirical Bayes Method. 10.5 Discussion. 11 Identical Reference Samples and Empirical Bayes Method for Cross-Batch Gene Expression Analysis ( Wynn L Walker and Frank R Sharp). 11.1 Introduction. 11.2 Methodology. 11.3 Application: Expression Profiling of Blood from Muscular Dystrophy Patients. 11.4 Discussion and Conclusion. 12 Principal Variance Components Analysis: Estimating Batch Effects in Microarray Gene Expression Data ( Jianying Li, Pierre R Bushel, Tzu-Ming Chu, and Russell D Wolfinger). 12.1 Introduction. 12.2 Methods. 12.3 Experimental Data. 12.4 Application of the PVCA Procedure to the Three Example Data Sets. 12.5 Discussion. 13 Batch Profile Estimation, Correction, and Scoring ( Tzu-Ming Chu, Wenjun Bao, Russell S Thomas, and Russell D Wolfinger). 13.1 Introduction. 13.2 Mouse Lung Tumorigenicity Data Set with Batch Effects. 13.3 Discussion. Acknowledgements. 14 Visualization of Cross-Platform Microarray Normalization ( Xuxin Liu, Joel Parker, Cheng Fan, Charles M Perou, and J S Marron). 14.1 Introduction. 14.2 Analysis of the NCI 60 Data. 14.3 Improved Statistical Power. 14.4 Gene-by-Gene versus Multivariate Views. 14.5 Conclusion. 15 Toward Integration of Biological Noise: Aggregation Effect in Microarray Data Analysis ( Lev Klebanov and Andreas Scherer). 15.1 Introduction. 15.2 Aggregated Expression Intensities. 15.3 Covariance between Log-Expressions. 15.4 Conclusion. Acknowledgements. 16 Potential Sources of Spurious Associations and Batch Effects in Genome-Wide Association Studies ( Huixiao Hong, Leming Shi, James C Fuscoe, Federico Goodsaid, Donna Mendrick, and Weida Tong). 16.1 Introduction. 16.2 Potential Sources of Spurious Associations. 16.3 Batch Effects. 16.4 Conclusion. Disclaimer. 17 Standard Operating Procedures in Clinical Gene Expression Biomarker Panel Development ( Khurram Shahzad, Anshu Sinha, Farhana Latif, and Mario C Deng). 17.1 Introduction. 17.2 Theoretical Framework. 17.3 Systems-Biological Concepts in Medicine. 17.4 General Conceptual Challenges. 17.5 Strategies for Gene Expression Biomarker Development. 17.6 Conclusions. 18 Data, Analysis, and Standardization ( Gabriella Rustici, Andreas Scherer, and John Quackenbush). 18.1 Introduction. 18.2 Reporting Standards. 18.3 Computational Standards: From Microarray to Omic Sciences. 18.4 Experimental Standards: Developing Quality Metrics and a Consensus on Data Analysis Methods. 18.5 Conclusions and Future Perspective. References. Index.

Empirical Bayes method Experimental data Bayes' theorem Data analysis Normalization (statistics) Gene expression profiling Spurious relationship Data set Statistics Computer science

Special Relationship"?" -- Harold Wilson, Lyndon B. Johnson And Anglo-american Relations 'at The Summit', 1964-8

“特殊关系”？：哈罗德·威尔逊，林登·贝恩斯·约翰逊和英美关系“在峰会上”，1964-1988

Manchester University Press Colman

ISBN：9780719070105，出版年：2004，中图分类号：D8

Drawing upon an extensive range of archival and secondary sources from both sides of the Atlantic, this pioneering book provides the first full-length study of the controversial personal relationship between Prime Minister Harold Wilson and President Lyndon B. Johnson, often drawing on material that has only recently been opened to the public. Whilst Wilson was a firm supporter of the idea of a 'special relationship' between Britain and the United States and wanted to use his dealings with the White House to strengthen his credentials as a world statesman, Johnson held the British leader in low esteem and disdained the idea of a 'special' Anglo-American relationship. Difficulties stemming from the Vietnam War, British economic weakness and the UK's abrogation of its world power status exacerbated the strain between Wilson and Johnson, leading to what was probably the most fractious and troubled of all the relationships between British prime ministers and American presidents. The work also explores the more general nature of Anglo-American bonds in this period, arguing that the impact of the substantive issues, along with the limitations of the relationship between Wilson and Johnson, led to a serious weakening of the high-level ties between Britain and the United States. This book will be of vital interest to students of British and US foreign policy, of Anglo-American relations, and summit diplomacy, as well as to those with an interest in Harold Wilson and Lyndon Johnson themselves.

Joking relationship Peer relationships Spurious relationship Onsager reciprocal relations Congruence relation Interpersonal ties Semantic relationship Interorganizational relations Correlation Thematic relation