05465nam 2200661Ia 450 991013995850332120170809171619.01-282-37950-X97866123795050-470-68598-00-470-68599-9(CKB)1000000000822292(EBL)470724(OCoLC)609849754(SSID)ssj0000335040(PQKBManifestationID)11251332(PQKBTitleCode)TC0000335040(PQKBWorkID)10271961(PQKB)10593108(MiAaPQ)EBC470724(EXLCZ)99100000000082229220091008d2009 uy 0engur|n|---|||||txtccrBatch effects and noise in microarray experiments, sources, and solutions[electronic resource] /edited by Andreas SchererChichester, West Sussex ;Hoboken J. Wiley20091 online resource (282 p.)Wiley Series in Probability and Statistics ;v.868Description based upon print version of record.0-470-74138-4 Includes bibliographical references and index.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 Scanning2.3.8 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 Design3.4 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 Designs4.3.3 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 Introduction7.1.1 Microarray Gene Expression DataBatch Effects and Noise in Microarray Experiments: Sources and Solutions looks at the issue of technical noise and batch effects in microarray studies and illustrates how to alleviate such factors whilst interpreting the relevant biological information. Each chapter focuses on sources of noise and batch effects before starting an experiment, with examples of statistical methods for detecting, measuring, and managing batch effects within and across datasets provided online. Throughout the book the importance of standardization and the value of standard operating procedures in the develWiley Series in Probability and StatisticsDNA microarraysDNA microarraysExperimentsElectronic books.DNA microarrays.DNA microarraysExperiments.572.8572.8636611.01816Scherer Andreas1966-854342MiAaPQMiAaPQMiAaPQBOOK9910139958503321Batch effects and noise in microarray experiments, sources, and solutions1907773UNINA