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Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/13845

Title: Gene Filtering in the Analysis of Illumina Microarray Experiments
Authors: Forcheh, Anyiawung Chiara
Verbeke, Geert
Kasim, Adetayo
Lin, Dan
Shkedy, Ziv
Talloen, Willem
Goehlmann, Hinrich W. H.
Clement, Lieven
Issue Date: 2012
Abstract: Illumina bead arrays are microarrays that contain a random number of technical replicates (beads) for every probe (bead type) within the same array. Typically around 30 beads are placed at random positions on the array surface, which opens unique opportunities for quality control. Most preprocessing methods for Illumina bead arrays are ported from the Affymetrix microarray platform and ignore the availability of the technical replicates. The large number of beads for a particular bead type on the same array, however, should be highly correlated, otherwise they just measure noise and can be removed from the downstream analysis. Hence, filtering bead types can be considered as an important step of the preprocessing procedure for Illumina platform. This paper proposes a filtering method for Illumina bead arrays, which builds upon the mixed model framework. Bead types are called informative/non-informative (I/NI) based on a trade-off between within and between array variabilities. The method is illustrated on a publicly available Illumina Spike-in data set (Dunning et al., 2008) and we also show that filtering results in a more powerful analysis of differentially expressed genes.
Notes: [Forcheh, Anyiawung Chiara; Verbeke, Geert; Lin, Dan; Shkedy, Ziv; Clement, Lieven] Katholieke Univ Leuven, Louvain, Belgium. [Lin, Dan; Shkedy, Ziv] Univ Hasselt, Interuniv Inst Biostat & Stat Bioinformat, Hasselt, Belgium. [Kasim, Adetayo] Univ Durham, Wolfson Res Inst, Durham DH1 3HP, England. [Talloen, Willem] Janssen Pharmaceut NV, Beerse, Belgium.
URI: http://hdl.handle.net/1942/13845
DOI: 10.2202/1544-6115.1710
ISI #: 000305579300003
ISSN: 2194-6302
Category: A1
Type: Journal Contribution
Validation: ecoom, 2013
Appears in Collections: Research publications

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