Tiling Microarray Analysis Tools 2 (T2)
Disclaimer: This software is distributed as is with no warrantee or guarantee of accuracy. See the original LBNL BDS License
Author: David Nix
What is T2?
T2 (aka TiMAT2) is a collection of software tools used for for both low and high level tiling microarray data analysis using the Affymetrix, NimbleGen, and Agilent platforms.
T2 is a fork of the original TiMAT project at the BDTNP.
T2 is designed for processing chIP-chip, RNA difference, and comparative genomic hybridization experiments from both single and multi chip data sets.
T2 was build over 3 years at LBNL and Affymetrix and is currently under further development at the Huntsman Cancer Institute's Bioinformatic Core Facility.
How to use T2?
To use T2, download the latest release, and launch the java jar applications with the -jar option.
For example, to execute 'ScanChip' type 'java -jar yourPathToTheT2Directory/T2/Apps/ScanChip' on the command line to print a menu and description of options.
- Usage - An outline/ tutorial on how to use T2 to process your tiling microarray data.
- Applications - A listing of the various T2 applications.
- Menus - Command line menus/ instructions/ parameters for each of the applications.
- Output File Type Descriptions - Description of the different types of file output generated by T2 applications.
- Fold vs Relative Difference - Conversion table for relative difference scores and fold different scores.
- JavaDocs - Code documentation for BioTools which includes T2. Eclipse users can directly import the T2 directory as an Eclipse project.
- LBNL BDS License - The original TiMAT license.
Don't hesitate to contact the Core with questions or comments.
- No java sourced or installed. Type 'java -version' on the command line. It should be >1.4.
- Not using the -jar option. Type: 'java -jar yourPathToTheT2Directory/T2/Apps/ScanChip'
- Out of memory error. Increase the heap size with the -Xmx flag. Type: 'java -jar -Xmx4000M yourPathToTheT2Directory/T2/Apps/ScanChip'
- Trying to run the apps on Windows. It is worth a try. These have been tested on Linux and Mac OSX.