Introduction

MOTIVATION: Many high-resolution array comparative genomic hybridization tumor profiles contain a wave bias, which makes accurate detection of breakpoints in such profiles more difficult. RESULTS: An efficient and highly effective algorithm that largely removes the wave bias from tumor profiles by regressing the tumor profile data on data of profiles from the clinical genetics practice. Results are illustrated on two independent datasets. The algorithm is shown to be robust against the presence of true copy number aberrations. Moreover, the smoothed profiles are able to recapitulate the aberration location and signal for simulated tumor profiles. AVAILABILITY: Easy-to-use R scripts, user instructions and data are available from http://www.few.vu.nl/~mavdwiel/nowaves.html. SUPPLEMENTARY INFORMATION: Supplementary information are available at Bioinformatics online.

Publications

  1. Smoothing waves in array CGH tumor profiles.
    Cite this
    van de Wiel MA, Brosens R, Eilers PH, Kumps C, Meijer GA, Menten B, Sistermans E, Speleman F, Timmerman ME, Ylstra B, 2009-05-01 - Bioinformatics (Oxford, England)

Credits

  1. Mark A van de Wiel
    Developer

  2. Rebecca Brosens
    Developer

  3. Paul H C Eilers
    Developer

  4. Candy Kumps
    Developer

  5. Gerrit A Meijer
    Developer

  6. Björn Menten
    Developer

  7. Erik Sistermans
    Developer

  8. Frank Speleman
    Developer

  9. Marieke E Timmerman
    Developer

  10. Bauke Ylstra
    Investigator

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Summary
AccessionBT006657
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByBauke Ylstra