beadarrayFilter: An R Package to Filter Beads

Authors

Anyiawung Chiara Forcheh, Katholieke Universiteit Leuven
Geert Verbeke, Katholieke Universiteit Leuven
Adetayo Kasim, Durham University
Dan Lin, Universiteit Hasselt
Ziv Shkedy, Universiteit Hasselt
Willem Talloen, Janssen Pharmaceutica N.V.
Hinrich W.H. Göhlmann, Janssen Pharmaceutica N.V.
Lieven Clement, Katholieke Universiteit Leuven

Date of this Version

6-2013

Document Type

Article

Citation

The R Journal (June 2013) 5(1); Editor: Hadley Wickham

Comments

Copyright 2013, The R Foundation. Open access material. License: CC BY 3.0 Unported

Abstract

Microarrays enable the expression levels of thousands of genes to be measured simultaneously. However, only a small fraction of these genes are expected to be expressed under different experimental conditions. Nowadays, filtering has been introduced as a step in the microarray pre-processing pipeline. Gene filtering aims at reducing the dimensionality of data by filtering redundant features prior to the actual statistical analysis. Previous filtering methods focus on the Affymetrix platform and can not be easily ported to the Illumina platform. As such, we developed a filtering method for Illumina bead arrays. We developed an R package, beadarrayFilter, to implement the latter method. In this paper, the main functions in the package are highlighted and using many examples, we illustrate how beadarrayFilter can be used to filter bead arrays.