Tiling Microarray Analysis Tools (TiMAT)

Disclaimer: This software is distributed as is with no warrantee or guarantee of accuracy. It is not endorsed or supported by Affymetrix. It is a collection of tools used in house for exploratory analysis. See the original LBNL BDS License.

System and Software Requirements


At this point there are a number of TiMAT releases and new releases should be regularly forthcoming for the foreseeable future. Multiple releases are simultaneously available which may have different utilities available or employ differing algorithms. While TiMAT is tested and intended to provide correct and rigorous processing, it is the user's responsibility to evaluate its performance on their data (please see the license).

The version numbering scheme works as follows:

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To install TiMAT v3.x.x, download the appropriate .zip file and unzip into the directory where you would like TiMAT to exist. TiMAT uses executable java jar files as well as jar libraries. The executables already contain the classpath info needed to find the necessary libraries. Therefore, it is important that the TiMAT files remain in the directory structure provided with the release. Executable jar files ignore classpath provided by environment variables or via the java command line -cp switch.

Next, the TiMAT directory contains a bin directory. These contain shell scripts to facilitate running TiMAT on unix-like plarforms. You may want to add the directory to your PATH environment variable. For instance, using the bash shell when TiMAT has been installed in /usr/local/TiMAT/:

shell$ export PATH=$PATH:/usr/local/TiMAT/bin

To run the qvalue analysis you will need R and the qvalue package. Consult the R homepage for installation instructions. To install the qvalue package, unzip and untar the qvalue_1.1.tar.gz file included with TiMAT. On a unix-like platform, try:

shell$ tar -zxvf qvalue_1.1.tar.gz

Windows users may want to try Cygwin or untar the file on a unix-like platform before moving the files to their window machine. Either way the qvalue must be in R's library path. Instructions for installing R packages can be found on the R website. To check if qvalue has been correctly installed, start the R environment and type library(). R will print out a list of installed packages, check that "qvalue" is among them. If R and qvalue are correctly installed, they will run automatically when TiMAT applications such as ScanChip need them.

Checking the Installation

If the installation has been successful, you should now be able to run TiMAT programs. If the PATH environment variable has been set and you are on a unix-like platform, try running one of the scripts in the TiMAT bin directory without any arguments. For example:

shell$ ScanChip

A help menu should be printed onto the screen. If you do not want to run the shell scripts or are running TiMAT on a Windows platform, change to the TiMAT directory and try:

shell$ java -jar lib/ScanChip.jar


Extensive documentation of the old TiMAT is available at LBNL. Don't hesitate to contact me with questions or comments.