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.


Common mistakes:

Don't hesitate to contact the Core with questions or comments.