Microarray Quality Control

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.