Gene Filtering in the Analysis of Illumina Microarray Experiments
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Anyiawung Chiara Forcheh
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.
©2012 Walter de Gruyter GmbH & Co. KG, Berlin/Boston
Articles in the same Issue
- Editorial Introduction
- Special Issue on Computational Statistical Methods for Genomics and Systems Biology
- Article
- A Generalized Hidden Markov Model for Determining Sequence-based Predictors of Nucleosome Positioning
- Gene Filtering in the Analysis of Illumina Microarray Experiments
- Principal Components of Heritability for High Dimension Quantitative Traits and General Pedigrees
- Bayesian Sparsity-Path-Analysis of Genetic Association Signal using Generalized t Priors
- A Family-Based Probabilistic Method for Capturing De Novo Mutations from High-Throughput Short-Read Sequencing Data
- Adjusting for Spurious Gene-by-Environment Interaction Using Case-Parent Triads
- Querying Genomic Databases: Refining the Connectivity Map
- A Model-Based Analysis to Infer the Functional Content of a Gene List
- Candidate Pathway Based Analysis for Cleft Lip with or without Cleft Palate
- Improving Pedigree-based Linkage Analysis by Estimating Coancestry Among Families
Articles in the same Issue
- Editorial Introduction
- Special Issue on Computational Statistical Methods for Genomics and Systems Biology
- Article
- A Generalized Hidden Markov Model for Determining Sequence-based Predictors of Nucleosome Positioning
- Gene Filtering in the Analysis of Illumina Microarray Experiments
- Principal Components of Heritability for High Dimension Quantitative Traits and General Pedigrees
- Bayesian Sparsity-Path-Analysis of Genetic Association Signal using Generalized t Priors
- A Family-Based Probabilistic Method for Capturing De Novo Mutations from High-Throughput Short-Read Sequencing Data
- Adjusting for Spurious Gene-by-Environment Interaction Using Case-Parent Triads
- Querying Genomic Databases: Refining the Connectivity Map
- A Model-Based Analysis to Infer the Functional Content of a Gene List
- Candidate Pathway Based Analysis for Cleft Lip with or without Cleft Palate
- Improving Pedigree-based Linkage Analysis by Estimating Coancestry Among Families
