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Correcting for probe-design in the analysis of gene-expression microarrays

The oligonucleotide probes on microarrays for gene expression are carefully designed so that their thermodynamic properties are consistent, in order that any bias due to differential efficiencies of hybridization might be minimized. However there are numerous other constraints such as the need to match (and be specific to) a gene, as well as possibly having a fixed probe length. Thus a perfect thermodynamic balance cannot be achieved. Also, since the labelling dyes can hinder hybridization, any thermodynamic balance achieved would not be robust to a change of the choice of dye, or method of adhering the dye to the RNA sample. Aside from Affymetrix platforms (Zhang et al. 2003, Abdueva et al. 2006), such effects are not usually accounted for when analysing the results of microarray experiments. In particular with two-channel platforms, one might anticipate that any effects would cancel out across the two channels. Here we focus on the Agilent Human 1A Oligo Microarray (V2), a popular twochannel array. We comment on the design of its probes, and illustrate the ways in which those designs can bias downstream analyses before discussing possible remedies.