1. Introduction
1.1 Microarrays & notation
1.2 Image quantification
1.3 Displays & plots
1.4 Analysis overview
1.5 Starting MAExplorer
1.6 Tutorials

2. MAExplorer menus
2.1 File Menu
2.2 Samples Menu
2.3 Edit Menu
2.4 Analysis Menu
2.4.1 GeneClass Menu
2.4.2 Normalization Menu
2.4.3 Filter Menu
2.4.4 Plot Menu
2.4.5 Cluster Menu
2.4.6 Report Menu
2.5 View Menu
2.6 Plugins Menu
2.7 Help Menu

3. Exploratory Analysis
3.1 Analysis objectives
3.2 Analysis steps
3.3 Gene intensity displays
3.4 Gene subsets
3.5 Sample conditions lists
3.6 Threshold sliders
3.7 Exporting data

4. Status and Bugs
4.1 Known Bugs
4.2 Revision Notes
4.3 Browser problems
4.4 Handling fatal errors

References
R.1 N.A.R. paper (PDF)
R.2 Overview (PDF)
R.3 Examples (PDF)
R.4 Use with mAdb (PDF)
R.5 Intro Data Mining (PDF)
R.6 Using Cvt2Mae to convert array data for use with MAExplorer.(PDF)
R.7 Statistics in Functional Genomics workshop paper (PDF)
R.8 Software design of the MAExplorer data mining tool (PDF) or (PPT)

Acknowledgments

Appendices
A. Short tutorial
B. Advanced tutorial

C. User's array data
C.1 Quantified spot data
C.2 Sample file format
C.3 Quant. file format
C.4 GIPO table format
C.5 Configuring tables
C.6 Using Cvt2Mae 'wizard'

D. Using stand-alone
D.1 Installing stand-alone
D.2 Downloading
D.3 Starting .mae files
D.4 Format .mae files
D.5 Using as Applet
D.6 Startup .mae files

E. Design Issues
E.1 Array data conversion
E.2 Client- vs. server-centric
E.3 Cvt2Mae data converter
E.4 MAExplorer plugins
E.5 Web DB server design
Glossary

List of Figures
List of Tables

Index

Help desk

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