Microarray Quality Control (PDF)

Foreword. Preface. 1. Quality of Biological Samples. 1.1 Tissue Acquisition, Handling, and Storage. 1.2 Pathological Evaluation. 1.3 Tissue heterogeneity and Laser Capture Microdissection. 1.4 Summary. 2. Microarray Production: Quality of DNA and Printing. 2.1 Quality Control for cDNA Probes. 2.2 Long-oligo Arrays. 2.3 Slide Coating. 2.4 Slide Autofluorescence. 2.5 Printing Quality Control. 2.6 Summary. 3. Quality of Microarray Hybridization. 3.1 RNA and cDNA Labeling Quality. 3.2 Specificity versus Sensitivity. 3.3 Amplification Strategies. 3.4 Indirect Labeling. 3.5 Automation of Microarray Hybridization. 3.6 Hybridization Reference. 3.7 Validation of Microarray Experiments. 3.8 Summary. 4. Scanners and Data Acquisition. 4.1 Basic Principles of Scanners. 4.2 Basic Principles of Imagers. 4.3 Calibration and PMT Gain. 4.4 Characteristics of Different Noise Sources. 5. Image Analysis. 5.1 Grid Alignment. 5.2 Spot Segmentation. 5.3 Extracting Information. 5.4 Appendix: Image Processing. 6. Quality Control in Data Analysis. 6.1 Normalization. 6.2 Replication. 6.3 Missing Values. 6.4 Data Management Issues. 6.5 Small-Sample-Size Issues. Index.

Wei Zhang, Ph.D., received his Ph.D. degree from The University of Texas Graduate School of Biomedical Sciences. He joined the faculty of M. D. Anderson Cancer Center in 1994 where he is currently an Associate Professor and the Director of the Cancer Genomics Core Laboratory. Dr. Zhang's research programs include cancer genomics and informatics, tumor suppressor genes, and signal transduction studies. Dr. Zhang has published over 100 peer-reviewed research papers, 14 book chapters and two books (Statistical and Computational Approaches to Genomcis, Genomic and Molecular Neuro-Oncology). Dr. Zhang is an Associate Editor for American Association of Cancer Research journal Clinical Cancer Research, and serves on editorial board of journals Cancer Biology and Therapy, Histology and Histopathology, International Journal of Oncology, BMC Genomics, Technology in Cancer Research and Treatment, and Molecular Cancer.

Ilya Shmulevich, Ph.D., received his Ph.D. degree in Electrical and Computer Engineering from Purdue University, West Lafayette, Indiana in 1997. In 1997-1998, he was a postdoctoral researcher at the Nijmegen Institute for Cognition and Information at the University of Nijmegen and National Research Institute for Mathematics and Computer Science at the University of Amsterdam in The Netherlands, where he studied computational models of music perception and recognition. In 1998-2000, he worked as a senior researcher at the Tampere International Center for Signal Processing at the Signal Processing Laboratory in Tampere University of Technology, Tampere, Finland. Presently, he is an Assistant Professor at the Cancer Genomics Laboratory at The University of Texas M. D. Anderson Cancer Center in Houston, TX. He is an Associate Editor of Environmental Health Perspectives: Toxicogenomics. His research interests include computational genomics, nonlinear signal and image processing, computational learning theory, and music recognition and perception.

Jaakko Astola,

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