Preprocessing and downstream analysis of microarray DNA copy number profiles

M.A. van de Wiel, F. Picard, W.N. van Wieringen, B. Ylstra

    Research output: Contribution to JournalArticleAcademicpeer-review

    Abstract

    Analysis of DNA copy number profiles requires methods tailored to the specific nature of these data. The number of available data analysis methods has grown enormously in the last 5 years. We discuss the typical characteristics of DNA copy number data, as measured by microarray technology and review the extensive literature on preprocessing methods such as segmentation and calling. Subsequently, the focus narrows to applications of DNA copy number in cancer, in particular, several downstream analyses of multi-sample data sets such as testing, clustering and classification. Finally, we look ahead: what should we prepare for and which methodology-related topics may deserve attention in the near future? © The Author 2010. Published by Oxford University Press.
    Original languageEnglish
    Pages (from-to)10-21
    JournalBriefings in bioinformatics
    Volume12
    Issue number1
    DOIs
    Publication statusPublished - 2011

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