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Microarray Quality Control

Wei Zhang, Ilya Shmulevich, Jaakko Astola

ISBN: 978-0-471-72854-2 January 2005 144 Pages


Microarray technology provides researchers in the life sciences with a revolutionary tool for measuring gene expression. However, this highly developed process involves multiple steps, from sample selection to data analysis, each susceptible to potentially costly errors. Without sound quality control, experimental microarrays may produce useless or, even worse, misleading results.
Microarray Quality Control provides a comprehensive resource for ensuring quality control in every step of this complex process. From experimental design to data processing, analysis, and interpretation, the emphasis in this text remains on practical advice 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 computational scientists-involved in microarray studies, Microarray Quality Control features a straightforward style easily accessed by various disciplines. Useful checklists and tips help ensure the integrity of results, and each chapter contains a thorough review of pertinent literature.
The only complete, systematic treatment of the topic available, Microarray Quality Control offers students and practitioners an invaluable resource for improving experimental quality and efficiency.


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.


"…a thought-provoking book…highly useful to statisticians, biologists, engineers, medical researchers, and medical scientists." (Journal of Statistical Computation and Simulation, September 2005)

"The book may be recommended for all researchers and students working with the DNA microarray technology" (Annals of Biomedical Engineering, June 2005)

"...a useful source of ideas and potential issues." (Journal of the American Statistical Association, June 2005)

"This book is recommended [for] all libraries serving researchers using high-throughput techniques." (E-STREAMS, March 2005)

“…an essential laboratory resource for scientists studying gene regulation and for all experimental biologists interested in the emerging practical applications of microarrays.” (Engineering in Life Sciences, Vol.5, No.5, 2004)

"…offers practical guidance for each stage of planning and execution of microarray studies…" (Genetic Engineering News, Vol. 24, No. 6, March 15, 2004)

"…the breadth of issues encompassed by quality control in microarray studies are covered…a valuable systematic treatment of microarray quality control." (Drug Discovery and Development, March 2004)