## aCGH / Test for copy number induced expression changes

### Description

Nonparametric testing for changes in expression induced by a change in DNA copy number. The copy number and expression probes of the two data sets must be matched together beforehand using the tool "Match copy number and expression probes".

### Parameters

- Test statistic to use (wcvm, wmw) [wcvm]
- Type of analysis (univariate, regional) [univariate]
- Number of permutations (...) [10000]

### Details

Performs a permutation-based non-parametric test to detect genes whose expression has been changed through a change in DNA copy number. Please see the referenced article for details on the two possible test statistics (weighted Cramer-Von Mises or weighted Mann-Whitney), and whether the test statistic should be "shrunken" within a region (regional), or not (univariate). Note that running this tool can take some hours depending on the size of the dataset.

### Output

A table of matched copy number and expression data, along with p-values of the permutation test. This file can be used to plot expression profiles of individual genes ("Plot copy-number-induced gene expression" tool).

### References

Wieringen et al. (2009) Nonparametric testing for DNA copy number induced differential mRNA gene expression. Biometrics 65: 19-29