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

ABSTRACT:

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 ar

SUBMITTER: Smith ML 

PROVIDER: S-EPMC2880029 | biostudies-literature | 2010 Apr

REPOSITORIES: biostudies-literature