Survey of Background Normalisation in Affymetrix Arrays and a Case Study

  • Vilda Purutçuoğlu
  • Elif Kayış
  • Gerhard-Wilhelm Weber
Part of the Studies in Computational Intelligence book series (SCI, volume 416)

Abstract

The oligonucleotide is a special type of one-channel microarrays which has 25-base pair long and the Affymetrix is the well-known oligonucleotide. In this study the normalisation procedure which enables us to discard the systematic erroneous signals in the measurements is described. Then different gene expression indices which are used to compute the true signals via the background normalisation are described in details. In these descriptions two recently suggested alternative approaches, namely frequentist (FGX) and robust (RGX) gene expression indices are explained besides the well-known approaches in this field. Finally a comparative analysis of the real microarray data with different sizes is presented to evaluate the performance of the underlying methods with RMA which is one of the common techniques in the analysis of microarray studies.

Keywords

Perfect Match Background Normalisation True Signal Probe Pair Affymetrix Array 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer Berlin Heidelberg 2012

Authors and Affiliations

  • Vilda Purutçuoğlu
    • 1
  • Elif Kayış
    • 2
  • Gerhard-Wilhelm Weber
    • 2
  1. 1.Department of StatisticsMiddle East Technical UniversityAnkaraTurkey
  2. 2.Institute of Applied MathematicsMiddle East Technical UniversityAnkaraTurkey

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