All software presented in this section is written by Mark van de Wiel, Department of Mathematics and Computer Science, Eindhoven University of Technology and Microarray facility, VU University Medical Center, Amsterdam, The Netherlands.

The software corresponds to the paper: "CGHMultiArray: Exact p-values for multi-array CGH-data"  by Mark A. van de Wiel, Serge J. Smeets,  Ruud H. Brakenhoff and Bauke Ylstra.  The paper has been accepted for publication in Bioinformatics. Complete reference will be given when the paper has been published. 

The web implementation CGHMultiArray allows anyone to compute exact p-values for discretized multi-array CGH-data per clone position. The test statistic is the Wilcoxon two-sample statistic with ties. A Mathematica licence is not needed to run this web implementation. The web implementation CGHMultiArrayRegion includes a simple method to define clone regions and p-value computation per clone region with FDR correction. 

Both implementations are also available as a Mathematica notebook.  The notebook can be used with hardly any knowledge of Mathematica, but, of course, a valid Mathematica licence is necessary. Evaluate the cells by clicking on them and pressing "Shift+Return". Confirm the initialization question when evaluating for the first time. The core algorithm of CGHMultiArray is also available as R code and program.

We provide a web tool to convert smoothed ratios resulting from CGH-Miner  and other smoothing programs (e.g. aCGHsmooth) to CGHMultiArray input.

Finally, technical details on the split-up algorithm, which is used to compute the p-values, and a comparison of this algorithm with a naive implementation is available.

Please, send any questions or remarks to: mark.vdwiel[at]vumc.nl.

Convert: Smooth-to-CGHMultiArray  

Web implementations and manuals: CGHMultiArray and CGHMultiArrayRegion

Mathematica Notebook (right-click for downloading): CGHMultiArrayNotebook.

R code and program: InstructionsRfiles   CGHMultiArrayR  SplitupAnnotated  SplitupAnnotated code

Technical information split-up algorithm and efficiency comparison: splitupdetails