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$ MPP Help   [ Version mpp-2.0 ]

This document describes how to install and use the MPP system for your chosen architecture:

Table of Contents
1. Introduction
1.1. About this document
1.2. Platforms
1.3. Copyright Information
1.4. Disclaimer
1.5. New Versions
1.6. Credits
1.7. Feedback
1.8. Translations
1.9. About the author
2. Prerequisites
2.1. Java
2.2. R, R packages and Rserve
2.3. JFreeChart
2.4. Machine specification
2.5. To build MPP
3. Installation
3.1. Prerequisite Installation
3.1.1. Linux/Unix
3.1.2. Windows
3.2. MPP Binary Installation
3.3. Building MPP from source
3.4. Example build.xml
3.5. Overview of paths and files
3.6. Operating System Issues
4. Using MPP
4.1. Shell scripts and Batch files
4.2. GUI or CLI?
4.3. Problems starting MPP?
5. mppGUI
5.1. Startup switches
5.2. File Menu Commands
5.2.1. Open GPR / CVS
5.2.2. Open XLS
5.2.3. Convert
5.2.4. Batch Convert
5.2.5. Export
5.2.6. Exit
5.3. Microarray Menu Commands
5.3.1. Analysis Settings
5.3.2. Analyse
5.3.3. Compare Matrices
5.4. Phylogeny Menu Commands
5.4.1. Prepare Data
5.5. Help Menu Commands
5.5.1. Help
5.5.2. About
5.6. Pop-up Menu Commands
5.6.1. Analysis Settings
5.6.2. Analyse
5.6.3. Export
5.6.4. Close Tab
5.6.5. Close All Tabs
6. mppCLI
6.1. CLI Commands
7. MPP Properties
7.1. MPP properties
7.2. LM properties
7.3. TAMLM properties
7.4. Phylogeny properties
8. Tutorial
8.1. My First MPP Analysis(TM)
8.2. Comparing matrices
8.3. Preparing data for phylogenetic analysis
9. MPP methodology in depth
9.1. Transforms
9.1.1. The log(2) transform
9.1.2. The arsinh transform
9.2. Analyses
9.2.1. mppLM
9.2.2. mppTAMLM
10. Developer's Corner
10.1. MPP Structure
10.2. Apache POI
10.3. Important Classes
10.3.1 xlParserApp
10.3.2 ExcelParser
10.3.3 CSVParser
10.3.3 GeneEntry
10.3.4 GeneEntryVector
10.3.5 mppAnalysisManager
10.3.6 mppLM
10.3.7 FindMj
10.3.8 IOUtils
10.3.9 mppUtils
10.3.10 Parameters
10.3.11 PluginManager
10.3.12 Transform
10.3.13 AbstractTransform
10.3.14 Analysis
10.3.15 AbstractAnalysis
10.4. Plugin Development
11. Known Bugs
© Rob Davey