DNA Microarray Data Analysis

Tuimala J., Laine M.M.952-9821-89-1

Table of contents :
Preface……Page 6
List of Contributors……Page 7
Contents……Page 8
Introduction……Page 15
What is a microarray?……Page 16
Microarray production……Page 17
Where can I obtain microarrays?……Page 18
RNA extraction from scarse tissue samples……Page 20
Scanning……Page 21
Typical research applications of microarrays……Page 22
Experimental design and controls……Page 23
Suggested reading……Page 24
Single Array analysis……Page 26
Signal algorithm……Page 27
Comparison analysis……Page 28
Change p-value……Page 29
Signal Log Ratio Algorithm……Page 30
Methodologies……Page 32
Genotype calls……Page 33
Suggested reading……Page 34
cDNA microarray data analysis……Page 35
Data analysis pipeline……Page 36
Choosing and using controls……Page 39
Choosing a technology platform……Page 40
Gene clustering v. gene classification……Page 41
Suggested reading……Page 42
Distribution……Page 43
Median……Page 44
Scatter plot……Page 45
Correlation (r)……Page 46
Linear regression……Page 47
Normal distribution……Page 48
Skewed distribution……Page 50
Checking the distribution of the data……Page 51
Transformation……Page 52
Outliers……Page 53
Missing values and imputation……Page 54
Basics of statistical testing……Page 55
Hypothesis pair……Page 56
Calculation of test statistic and degrees of freedom……Page 57
Multiple testing……Page 58
Completely randomized experiment……Page 59
Scatter plot and histogram……Page 61
Linear regression……Page 62
Independent samples t-test and ANOVA……Page 63
Suggested reading……Page 65
Analysis……Page 66
Missing values……Page 67
Checking the background reading……Page 69
Intensity ratio……Page 70
Log ratio……Page 71
Time series……Page 72
Checking the quality of replicates……Page 73
Excluding bad replicates……Page 74
Filtering bad data……Page 75
Filtering uninteresting data……Page 77
Skewness and normality……Page 78
Linearity……Page 79
Spatial effects……Page 80
Similarity of dynamic range, mean and variance……Page 82
Replicates……Page 83
Filtering……Page 84
Suggested reading……Page 85
Scanner malfunction……Page 86
Plate and reporter effects……Page 87
Normalization terminology……Page 88
Normalization, standardization and centralization……Page 89
Choice of the method……Page 90
Control genes……Page 91
Special situations……Page 92
Standardization……Page 93
Lowess smoothing……Page 94
Dye-swap experiments……Page 95
Example of calculations……Page 96
Using GeneSpring for normalization……Page 97
Suggested reading……Page 99
Statistical single chip methods……Page 101
Sapir and Churchill’s single slide method……Page 102
Chen’s single slide method……Page 103
Newton’s single slide method……Page 104
Only some treatments have replicates……Page 105
All the treatments have replicates: two-sample t-test……Page 106
GeneSpring examples……Page 107
Suggested reading……Page 108
Principles of clustering……Page 109
Hierarchical clustering……Page 110
Self-organizing map……Page 111
K-means clustering……Page 112
Principal component analysis……Page 113
Pros and cons of clustering……Page 114
Visualization……Page 115
Programs for clustering and visualization……Page 117
Clustering tool……Page 118
Principal components analysis tool……Page 119
Suggested reading……Page 120
Data mining……Page 121
Fundamentals……Page 122
Bayesian network……Page 124
Calculating Bayesian network parameters……Page 125
Searching Bayesian network structure……Page 127
Conclusion……Page 128
Suggested reading……Page 129
Introduction……Page 130
Finding promoter region sequences……Page 131
Using EnsMart to retrieve promoter regions……Page 134
Comparison of EnsMart and UCSC searches……Page 136
Pattern search without prior knowledge……Page 138
GeneSpring and promoter analysis……Page 139
Suggested reading……Page 140
Retrieving annotations from public databases……Page 141
Article mining……Page 142
Ontologies……Page 143
Tools and data management……Page 145
What details should be reported: the MIAME standard……Page 146
MAGE-ML; an XML-translation of MAGE-OM……Page 148
MIAMExpress……Page 149
Other options and aspects……Page 150
Suggested reading……Page 151
A standard file format……Page 153
Awk……Page 154
Freeware software packages……Page 155
Bioconductor……Page 156
J-Express……Page 157
Spotfire……Page 158
Index……Page 159