Introduction

An algorithm to reduce multi-sample array CGH data from thousands of clones to tens or hundreds of clone regions is introduced. This reduction of the data is performed such that little information is lost, which is possible due to the high dependencies between neighboring clones. The algorithm is explained using a small example. The potential beneficial effects of the algorithm for downstream analysis are illustrated by re-analysis of previously published colorectal cancer data. Using multiple testing corrections suitable for these data, we provide statistical evidence for genomic differences on several clone regions between MSI+ and CIN+ tumors. The algorithm, named CGHregions, is available as an easy-to-use script in R.

Publications

  1. CGHregions: dimension reduction for array CGH data with minimal information loss.
    Cite this
    van de Wiel MA, Wieringen WN, 2007-02-01 - Cancer informatics

Credits

  1. Mark A van de Wiel
    Developer

    Department of Pathology and Department of Biostatistics (KEB), VU University Medical Center

  2. Wessel N van Wieringen
    Investigator

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Summary
AccessionBT001602
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByWessel N van Wieringen