beadarrayFilter: An R Package to Filter Beads

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 preprocessing 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.

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“…We selected probes for the training set using the intra-class correlation (ICC) method provided by the R beadarrayFilter package. (24) We used a cutoff of 0.5 to select probes for which the between array variability exceeded the within array variability. This package and cutoff value have been demonstrated to produce more powerful analysis of differentially expressed genes on a publicly available Illumina Spike-in expression set.…”