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A Practical Guide to Scientific Data Analysis

ISBN: 978-0-470-68481-8
358 pages
December 2009
A Practical Guide to Scientific Data Analysis  (047068481X) cover image

Description

Inspired by the author's need for practical guidance in the processes of data analysis, A Practical Guide to Scientific Data Analysis has been written as a statistical companion for the working scientist.  This handbook of data analysis with worked examples focuses on the application of mathematical and statistical techniques and the interpretation of their results.

Covering the most common statistical methods for examining and exploring relationships in data, the text includes extensive examples from a variety of scientific disciplines.

The chapters are organised logically, from planning an experiment, through examining and displaying the data, to constructing quantitative models. Each chapter is intended to stand alone so that casual users can refer to the section that is most appropriate to their problem.

Written by a highly qualified and internationally respected author this text:

  • Presents statistics for the non-statistician
  • Explains a variety of methods to extract information from data
  • Describes the application of statistical methods to the design of “performance chemicals”
  • Emphasises the application of statistical techniques and the interpretation of their results

Of practical use to chemists, biochemists, pharmacists, biologists and researchers from many other scientific disciplines in both industry and academia.

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Table of Contents

Preface xi

Abbreviations xiii

1 Introduction: Data and Its Properties, Analytical Methods and Jargon 1

1.1 Introduction 2

1.2 Types of Data 3

1.3 Sources of Data 5

1.3.1 Dependent Data 5

1.3.2 Independent Data 6

1.4 The Nature of Data 7

1.4.1 Types of Data and Scales of Measurement 8

1.4.2 Data Distribution 10

1.4.3 Deviations in Distribution 15

1.5 Analytical Methods 19

1.6 Summary 23

References 23

2 Experimental Design – Experiment and Set Selection 25

2.1 What is Experimental Design? 25

2.2 Experimental Design Techniques 27

2.2.1 Single-factor Design Methods 31

2.2.2 Factorial Design (Multiple-factor Design) 33

2.2.3 D-optimal Design 38

2.3 Strategies for Compound Selection 40

2.4 High Throughput Experiments 51

2.5 Summary 53

References 54

3 Data Pre-treatment and Variable Selection 57

3.1 Introduction 57

3.2 Data Distribution 58

3.3 Scaling 60

3.4 Correlations 62

3.5 Data Reduction 63

3.6 Variable Selection 67

3.7 Summary 72

References 73

4 Data Display 75

4.1 Introduction 75

4.2 Linear Methods 77

4.3 Nonlinear Methods 94

4.3.1 Nonlinear Mapping 94

4.3.2 Self-organizing Map 105

4.4 Faces, Flowerplots and Friends 110

4.5 Summary 113

References 116

5 Unsupervised Learning 119

5.1 Introduction 119

5.2 Nearest-neighbour Methods 120

5.3 Factor Analysis 125

5.4 Cluster Analysis 135

5.5 Cluster Significance Analysis 140

5.6 Summary 143

References 144

6 Regression Analysis 145

6.1 Introduction 145

6.2 Simple Linear Regression 146

6.3 Multiple Linear Regression 154

6.3.1 Creating Multiple Regression Models 159

6.3.1.1 Forward Inclusion 159

6.3.1.2 Backward Elimination 161

6.3.1.3 Stepwise Regression 163

6.3.1.4 All Subsets 164

6.3.1.5 Model Selection by Genetic Algorithm 165

6.3.2 Nonlinear Regression Models 167

6.3.3 Regression with Indicator Variables 169

6.4 Multiple Regression: Robustness, Chance Effects, the Comparison of Models and Selection Bias 174

6.4.1 Robustness (Cross-validation) 174

6.4.2 Chance Effects 177

6.4.3 Comparison of Regression Models 178

6.4.4 Selection Bias 180

6.5 Summary 183

References 184

7 Supervised Learning 187

7.1 Introduction 187

7.2 Discriminant Techniques 188

7.2.1 Discriminant Analysis 188

7.2.2 SIMCA 195

7.2.3 Confusion Matrices 198

7.2.4 Conditions and Cautions for Discriminant Analysis 201

7.3 Regression on Principal Components and PLS 202

7.3.1 Regression on Principal Components 203

7.3.2 Partial Least Squares 206

7.3.3 Continuum Regression 211

7.4 Feature Selection 214

7.5 Summary 216

References 217

8 Multivariate Dependent Data 219

8.1 Introduction 219

8.2 Principal Components and Factor Analysis 221

8.3 Cluster Analysis 230

8.4 Spectral Map Analysis 233

8.5 Models with Multivariate Dependent and Independent Data 238

8.6 Summary 246

References 247

9 Artificial Intelligence and Friends 249

9.1 Introduction 250

9.2 Expert Systems 251

9.2.1 LogP Prediction 252

9.2.2 Toxicity Prediction 261

9.2.3 Reaction and Structure Prediction 268

9.3 Neural Networks 273

9.3.1 Data Display Using ANN 277

9.3.2 Data Analysis Using ANN 280

9.3.3 Building ANN Models 287

9.3.4 Interrogating ANN Models 292

9.4 Miscellaneous AI Techniques 295

9.5 Genetic Methods 301

9.6 Consensus Models 303

9.7 Summary 304

References 305

10 Molecular Design 309

10.1 The Need for Molecular Design 309

10.2 What is QSAR/QSPR? 310

10.3 Why Look for Quantitative Relationships? 321

10.4 Modelling Chemistry 323

10.5 Molecular Fields and Surfaces 325

10.6 Mixtures 327

10.7 Summary 329

References 330

Index 333

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Reviews

“Written by a highly qualified internationally respected author this text is of practical use to chemists, biochemists, pharmacists, biologists and researchers from many other scientific disciplines in both industry and academia.”  (International Journal Microstructure & Materials Properties, 1 October 2011)

"At the same time, the highly detailed, thoughtful and readable explanation of statistical and data-mining concepts throughout the book will make it a valuable addition to the libraries of a wide range of researchers . . . It is definitely worth its purchase price and may be considered seriously as a textbook for nonmajor statistics students and research scientists in a wide variety of fields." (The American Statistician, 1 May 2011)

"The book is recommended for readers interested, but not experienced, in data analysis methods used in drug design, pharmaceutical research or related areas. It provides an almost mathematical-free introduction to some multivariate statistical methods applied in these fields. Also the great experience and the personal views of a highly qualified author may be interesting for many scientists." (Zentralblatt Math, 2010)

"This book should provide those engaged in multidimensional experimentation a relatively compact (under 400 pages) oversight of the relative merits of numerous techniques, all of which are heavily computer dependent, and will be of especial interest to those working in the field of pharmaceutical research. It should also draw their attention to the roots of complex methods by means of its introductory chapters." (Chromatographia, October 2010)

"This book is a guide to the wide range of methods available. Not surprisingly given the author’s background, the examples in the book are all chemical and hence it will be of most interest and value to chemistry researchers.” (Chemistry World, May 2010)

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