Zhang / Shmulevich / Astola Microarray Quality Control

1. Auflage 2005
ISBN: 978-0-471-72624-1
Verlag: John Wiley & Sons
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 160 Seiten, E-Book

Microarray technology provides researchers in the life scienceswith a revolutionary tool for measuring gene expression. However,this highly developed process involves multiple steps, from sampleselection to data analysis, each susceptible to potentially costlyerrors. Without sound quality control, experimental microarrays mayproduce useless or, even worse, misleading results.
Microarray Quality Control provides a comprehensive resource forensuring quality control in every step of this complex process.From experimental design to data processing, analysis, andinterpretation, the emphasis in this text remains on practicaladvice for each stage of planning and running a microarray study.Chapters cover:
* Quality of biological samples
* Quality of DNA
* Hybridization protocols Scanning
* Data acquisition
* Image analysis
* Data analysis
Written for the broad group of workers-biologists, mathematicians,statisticians, engineers, physicians, and computationalscientists-involved in microarray studies, Microarray QualityControl features a straightforward style easily accessed by variousdisciplines. Useful checklists and tips help ensure the integrityof results, and each chapter contains a thorough review ofpertinent literature.
The only complete, systematic treatment of the topic available,Microarray Quality Control offers students and practitioners aninvaluable resource for improving experimental quality andefficiency.

Autoren/Hrsg.

Zhang, Wei

Shmulevich, Ilya

Astola, Jaakko

Inhaltsverzeichnis

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 andPrinting.
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.

Über Autor(innen)

Wei Zhang, Ph.D., received his Ph.D. degree fromThe University of Texas Graduate School of BiomedicalSciences. He joined the faculty of M. D. Anderson CancerCenter in 1994 where he is currently an Associate Professor and theDirector of the Cancer Genomics Core Laboratory. Dr. Zhang'sresearch programs include cancer genomics and informatics, tumorsuppressor genes, and signal transduction studies. Dr. Zhang haspublished over 100 peer-reviewed research papers, 14 book chaptersand two books (Statistical and Computational Approaches toGenomcis, Genomic and Molecular Neuro-Oncology). Dr. Zhang is anAssociate Editor for American Association of Cancer Researchjournal Clinical Cancer Research, and serves on editorial board ofjournals Cancer Biology and Therapy, Histology and Histopathology,International Journal of Oncology, BMC Genomics, Technology inCancer Research and Treatment, and Molecular Cancer.
Ilya Shmulevich, Ph.D., received his Ph.D. degree inElectrical and Computer Engineering from Purdue University, WestLafayette, Indiana in 1997. In 1997-1998, he was a postdoctoralresearcher at the Nijmegen Institute for Cognition and Informationat the University of Nijmegen and National Research Institute forMathematics and Computer Science at the University of Amsterdam inThe Netherlands, where he studied computational models of musicperception and recognition. In 1998-2000, he worked as asenior researcher at the Tampere International Center for SignalProcessing at the Signal Processing Laboratory in TampereUniversity of Technology, Tampere, Finland. Presently, he is anAssistant Professor at the Cancer Genomics Laboratory at TheUniversity of Texas M. D. Anderson Cancer Center in Houston, TX. Heis an Associate Editor of Environmental Health Perspectives:Toxicogenomics. His research interests include computationalgenomics, nonlinear signal and image processing, computationallearning theory, and music recognition and perception.
Jaakko Astola, Ph.D., received his B.Sc., M.Sc.and Ph.D. degrees from Turku University, Finland. He has worked atTurku University, the Research Institute for Mathematical Sciencesof Kyoto University, Kyoto, Japan, Lappeenranta University ofTechnology, Lappeenranta, Finland, and Eindhoven University ofTechnology, The Netherlands. From 1987 to 1992 he was AssociateProfessor in Applied Mathematics at Tampere University, Tampere,Finland. From 1993 he has been Professor of Signal Processing atTampere University of Technology leading a group of about 60scientists and was nominated Academy Professor by Academy ofFinland (2001-2006). His research group was elected as a Centre ofExcellence in Research by the Academy of Finland for the years2000-2005. He is also director of Tampere International Center forSignal Processing (founded 1997) that has already hosted numerousvisiting scientists in Signal Processing as well as organizedworkshops and conferences. He has about 25 years of experience inteaching both undergraduate and graduate level. He has likewise 25years of experience in scientific research in mathematics,communications theory, and signal processing. He has authored over400 papers and four textbooks on signal processing and itsapplications.