Table of content
Acknowledgements Introduction
Chapter 0: Background
1 A SHORT INTRODUCTION TO THE RELEVANT BIOLOGY...0-1
2 THE MICROARRAY TECHNOLOGY ...0-3
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3 AN EXAMPLE FROM THE IRIBHM LABORATORY...0-6
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4 A PRIMER ON CLUSTERING ...0-8
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5 CONCLUSION ...0-13 6 REFERENCES ... 0-13
Chapter 1: Determination of differentially expressed genes
1 INTRODUCTION...1-1 2 DETERMINATION OF THE P-VALUES ...1-2
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3 CORRECTION FOR MULTI-TESTING ...1-11
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4 APPLICATION TO THE THYROID DATA SET ...1-19
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5 CONCLUSION ...1-21
6 REFERENCES ...1-22
Chapter 2: Data quality improvement
1 INTRODUCTION... 2-1 2 ASSESSING THE EFFECT OF A MODIFICATION ... 2-1
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3 MERGING OF SCANS OF DIFFERENT GAINS... 2-4
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4 EFFECT OF COLOR-FLIP ... 2-8 5 BACKGROUND CORRECTION ... 2-9 6 NORMALIZATION ... 2-10
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7 CONCLUSION ... 2-14 8 BIBLIOGRAPHY ... 2-15
Chapter 3: A database for microarray data
1 INTRODUCTION... 3-1
2 ONE SIZE FITS IT ALL... 3-1 4
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3 THE DATABASE ... 3-6
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4 DISCUSSION ... 3-10 5 BIBLIOGRAPHY ... 3-10
Chapter 4: Discovery of overlapping clustering
1 INTRODUCTION... 4-1 2 METHODS ... 4-2
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3 RESULTS... 4-6
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4 CONCLUSION ... 4-14 5 APPENDIX – NORMALIZATION PROCEDURES ... 4-15 6 BIBLIOGRAPHY ... 4-16
Chapter 5:Mathematical dissection of heterogeneous samples
1 INTRODUCTION... 5-1 2 GENERAL FRAMEWORK FOR THE SOLUTION... 5-1
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3 ALGORITHMS ... 5-4
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4 SIMULATION ... 5-6 5 CORRELATION ... 5-7
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6 RESULTS WITH REAL DATA... 5-8
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7 CONCLUSION ... 5-11 8 BIBLIOGRAPHY ... 5-11
Chapter 6: Genetic network inference
1 INTRODUCTION...6-1 2 THE BINARY SWITCH MODEL...6-2 3 IDENTIFICATION OF THE MODEL...6-4
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4 APPLICATION: ARTIFICIAL DATA...6-8 5 APPLICATION: REAL DATA...6-9
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6 CONCLUSION ...6-11 7 REFERENCES ...6-12
