Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data

Background: A key stage for all microarray analyses is the extraction of feature-intensities from an image. If this step goes wrong, then subsequent preprocessing and processing stages will stand little chance of rectifying the matter. Illumina employ random construction of their BeadArrays, making feature-intensity extraction even more important for the Illumina platform than for other technologies. In this paper we show that using raw Illumina data it is possible to identify, control, and perhaps correct for a range of spatial-related phenomena that affect feature-intensity extraction. Results: We note that feature intensities can be unnaturally high when in the proximity of a number of phenomena relating either to the images themselves or to the layout of the beads on an array. Additionally we note that beads neighbour beads of the same type more often than one might expect, which may cause concern in some models of hybridization. We highlight issues in the identification of a bead...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Mike L. Smith, Mark J. Dunning, Simon Tavaré, Andy G. Lynch
• Keywords: Beads, BMCBI 2010, Business, Image, Microarray Analyses