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Contents
Contents
VAMP
Administration and User Manual
Version 1.4.39
June 18, 2008
Visualization and Analysis of CGH arrays, transcriptome and other Molecular Profiles
Institut Curie Bioinformatics Unit
Contents
1. Introduction
2. Administration manual
2.1 System requirements
2.2 Installation and configuration
2.2.1 Installation
2.2.2 How to launch VAMP
2.2.3 Configuration
2.2.3.1 Administrator configuration
2.2.3.2 User configuration
2.2.4 Data format
2.2.4.1 Scripts for automated data generation
2.2.4.2 Array files
2.2.4.3 Sample annotation data
3. User Manual
3.1 Overview
3.1.1 Top-left frame
3.1.2 Bottom-left frame
3.1.3 Main frame
3.2 Basic functions
3.2.1 Data import
3.2.2 Data display
3.2.2.1 Profile View
3.2.2.2 Karyotype View
3.2.2.3 Dot Plot View
3.2.2.4 List View
3.2.2.5 Display additional features
3.2.3 Search
3.2.3.1 Search for arrays
3.2.3.2 Search for elements
3.2.4 Visual rendering
3.2.4.1 Zoom
3.2.4.2 Color codes
3.2.4.3 X and Y scaling
3.2.5 Print
3.2.6 Save and load
3.3 Data analysis
3.3.1 Manual analysis
3.3.2 FrAGL (Frequency of Amplicon, Gain and Loss) view
3.3.3 Finding common alterations among a collection of CGH- array profiles
3.3.4 Clustering profiles
3.3.5 Comparing profiles
3.3.6 Confrontation with sample annotation
3.3.7 Synteny analysis
3.3.8 Confrontation with Genome Annotation
3.3.9 Signal Histogram
3.3.10 Differential Analysis
3.3.11 Correlation Analysis
3.3.11.1 Calculating correlations
3.3.11.2 Visualizing results
3.3.11.3 Exporting the results
4. Analysis example - Bladder Cancer
4.1 Introduction
4.2 Import the genomic profiles
4.3 Minimal Alteration computation
4.3.1 Parameters settings
4.3.2 Visualization of the regions
4.3.3 Visualization of the samples with the alteration
4.3.4 Candidate genes
4.4 Genome/Transcriptome comparison
5. Analysis example - Colon Cancer
5.1 Introduction
5.2 Import the genomic profiles
5.3 Frequency alteration computation
5.3.1 Computation for each dataset
5.3.2 Comparison of the frequency between the two datasets
6. Availability
7. How to cite us?
Bibliography
8. Annexes
8.1 Main configuration XML file
8.2 Sample user configuration XML file
8.3 Import XML file
8.4 CGH array XML file
8.5 Transcriptome array XML file
About this document ...
2007 - Institut Curie Bioinformatics unit
