A repeated measures microarray design with 22 healthy, non-smoking volunteers (aging 32±5years) was set up to study transcriptome profiles in whole blood samples. The results indicate that repeatable data can be obtained with high within-subject correlation. Probes that could discriminate between individuals are associated with immune and inflammatory functions. When investigating possible time trends in the microarray data, we have found no differential expression within a sampling period (within-season effect). Differential expression was observed between sampling seasons and the data suggest a weak response of genes related to immune system functioning. Finally, a high number of probes showed significant season-specific expression variability within subjects. Expression variability increased in springtime and there was an association of the probe list with immune system functioning. Our study suggests that the blood transcriptome of healthy individuals is reproducible over a time period of several months.

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.

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.