Foreword
Overview
Demonstrations
Open source
Download
Documentation
Manual
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Assumptions
Overview
Menu summary
Quick start
1. Introduction
1.1 Microarrays and 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 Convert array data (PDF)
R.7 S.F.G. paper (PDF)
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
List of
Figures
List of
Tables
Downloading MAExplorer
Data format conversion
Plugin Extensions
Open Source