Download the software
The program is written entirely in Java, so it can be run on all operating systems. To run it you must first have the Java run time environment installed. To see if java is already installed, open a command prompt (Start->Run->cmd) and type “java –version”. If Java is found and the version is 1.4.1 and up, you can go ahead and download the program. If not install the Java run time environment (JRE) from here.
After installing the JRE download our program from here.
To run the original non-weighted version type:
java -jar TNoM.jar [labels and expression filename] [output filename]
for example: java -jar TNoM.jar rawData700x42.txt output.txt
To run the weighted (attached) version type:
java -jar TNoM.jar [labels and expression filename] [output filename] [weights file name] [optional: number of different weights]
Labels and expression filename:
The gene expression levels file is a text delimited text file. The first line should contain the classifications: either ‘+’ or ‘-‘. From the second line and on the first column is the gene name and the rest are the expression levels. For an example file, click here.
A filename to which the output will be saved.
The weights file is a text delimited text file. It should contain the weights corresponding to the gene expression levels file. The first line corresponds to the first gene etc. For an example file, click here.
The weights in the weights file are transformed into discrete weights. The options are either 4 or 10. Choosing 4 means 4 discrete weights, not including 0 - 0, 0.25, 0.5, 0.75 and 1. Choosing 10 means 10 discrete weights (not including 0) – 0, 0.1, 0.2 and so on. If not supplied the default is 4. Choosing 10 will greatly increase the time and memory needed for the calculation.
If you get an outOfMemory exception, and you have at least 512MB of RAM, you can increase the amount of memory java uses by adding “-Xmx384M” after “java”.