Case/Control Prediction from Illumina Methylation Microarray’s β and Two-Color Channels in the Presence of Batch Effects

  • Fabrice Colas
  • Jeanine J. Houwing-Duistermaat
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7548)


Among the published studies that submitted Illumina BeadArray 27k methylation datasets to the Gene Expression Omnibus (GEO), more than nine out of ten analyse β, thus making β a de facto standard. Further, as β combines the two color channels M and U into the ratio M/(M + U), we also assume, maybe naively, that β conveys more biologically relevant information than a single color taken alone. As well, a fourth of the GEO studies do not report any analysis step to cancel for non-biological variation. Here, we farther assess the validity of β as a micro array methylation analysis measure by testing empirically whether β predicts more accurately the case/control status than the two color channels taken independently. In addition, we consider whether cancelling the non-biological effects due to the genotyping protocol influences the prediction accuracy. Our results show that M alone predicts better than β and U, interpreting that U’s low prediction impacts negatively the one of β. We also confirm that without proper batch effect cancellation, non-biological variance hides the biological signal, making impractical the prediction of case status.


DNA Methylation Microarray Batch Effect Prediction 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Fabrice Colas
    • 1
  • Jeanine J. Houwing-Duistermaat
    • 1
  1. 1.MEDSTATSLeiden University Medical CenterLeidenThe Netherlands

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