"Harshlighting" small blemishes on microarrays

We present a method that harnesses the statistical power provided by having several HDONAs available, which are obtained under similar conditions except for the experimental factor. This method "harshlights" blemishes and renders them evident. We find empirically that about 25% of our chips are blemished, and we analyze the impact of masking them on screening for differentially expressed genes.Experiments attempting to assess subtle expression changes should be carefully screened for blemishes on the chips. The proposed method provides investigators with a novel robust approach to improve the sensitivity of microarray analyses. By utilizing topological information to identify and mask blemishes prior to model based analyses, the method prevents artefacts from confounding the process of background correction, normalization, and summarization.Analysis of hybridized microarrays starts with scanning the fluorescent image. For high-density oligonucleotide arrays (HDONAs) such as Affymetrix GeneChip？ oligonucleotide (Affy) arrays, the focus of this paper, each scanned image is stored pixel-by-pixel in a 'DAT' file. As the first step in measuring intensity of the hybridization signal, a grid is overlaid, the image is segmented into spots or features, and the pixel intensities within each of these are summarized as a probe intensity estimate (See reviews [1] and [2] for cDNA chips). The probe-level intensity estimates are stored in a 'CEL' file. Each gene is represented by pairs of probes, each representing another characteristic sequences and a 'mismatch', which is identical, except for the Watson-Crick complement in the center. Expression of a gene is estimated from such a probe set by applying algorithms for background correction, normalization, and summarization.The quality of data scanned from a microarray is affected by a plethora of potential confounders, which may act during printing/manufacturing, hybridization, washing, and reading. Each chip contains a number of