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      • Faculty of Science
      • Department of Molecular Biology and Genetics
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      Investigation and comparison of the preprocessing algorithms for microarray analysis for robust gene expression calculation and performance analysis of technical replicates

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      Author
      İlk, H. G.
      İlk, Ö.
      Konu, Özlen
      Özdağ, H.
      Date
      2006
      Source Title
      Proceedings of the IEEE 14th Signal Processing and Communications Applications Conference, SIU 2006
      Print ISSN
      2165-0608
      Publisher
      IEEE
      Volume
      2006
      Language
      Turkish
      Type
      Conference Paper
      Item Usage Stats
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      119
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      Abstract
      Preprocessing of microarray data involves the necessary steps of background correction, normalization and summarization of the raw intensity data obtained from cDNA or oligo-arrays before statistical analysis. Several algorithms, namely RMA, dChip, and MAS5 exist for the preprocessing of Affymetrix microarray data. Previous studies have identified RMA as one of most accurate algorithms while MAS5 was characterized with lower accuracy and sensitivity levels. In this study, performance of different preprocessing algorithms have been compared in terms of ROC characteristics of pairwise intensity differences of microarray replicates. Our findings indicated that all three algorithms predicted in similar order the quality of the technical replicates obtained from a selected set of latin square experiments [1]. On the other hand, RMA exhibited higher performance in terms of accuracy by maximizing the area under the receiver operating curve. The proposed method also is useful for detection of global and/or local artifacts associated within the technical replicas of a microarray experiment. Therefore this study is unique in the sense that it provides an extensive investigation and comparison of preprocessing algorithms and proposes a novel method for the detection and identification of fine technical replicate pair.
      Keywords
      Performance analysis
      Preprocessing algorithms
      Receiver operating curves
      Algorithms
      DNA
      Gene expression
      Optimization
      Sensitivity analysis
      Signal receivers
      Microarrays
      Permalink
      http://hdl.handle.net/11693/27183
      Published Version (Please cite this version)
      http://dx.doi.org/10.1109/SIU.2006.1659873
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