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