MatArray toolbox

What is it?

The MatArray toolbox is a set of Matlab tools designed for the analysis of microarray data. Its main features are: The toolbox is geared towards seasonned Matlab users, who want to treat microarray data with efficient command-line algorithms.

For more information, you can take a look at the start-up guide or at the reference. Both can be downloaded as indicated below.

The toolbox has been described in an application note published in Bioinformatics, 19, 659-660 (there are limitations imposed by Bioinformatics on what you can do with that paper).

License information

The toolbox is free for any use, commercial or otherwise, in its original or in a modified form, as long as proper credit is given.

Installation

Note

For efficiency, some algorithms are coded in C. This means that some files should be compiled using the mex function. For commodity, a win32 version with pre-compiled binaries is also available.

Downloads

And then...

For the toolbox, unzip in a directory and change your path so that it encompasses that directory.

To compile the mex-files, move to the directory cfiles in the matarray directory and type MatArrayCompile. Everything should go just fine if the compiler is properly set up. A C++ compiler is needed for the leaf ordering routine.

For the help files, unzip to a directory and open "matoc.html" in you web browser. In order for the links to the Matlab help files to work, the files should be unzipped to the directory MATLAB/help/toolbox/matarray.

Update

The toolbox and the help files have been updated (march 3rd 2003).

Who is guilty for this?

The toolbox was written for the most part by David Venet, except for the leaf ordering routine which is based on a code from Ziv Bar-Joseph.

Bug report, suggestions, improvements,...

Please drop an e-mail to David Venet.