Fully Automatic Quantification of Microarray Image Data

摘要: DNA microarrays are now widely used to measure expression levels and copy number in biological samples. Ratios of relative abundance nucleic acids derived from images regular arrays spots containing target genetic material which fluorescently labeled samples hybridized. Whereas there a methods use for the quantification images, many software systems wide either encourage or require extensive human interaction at level individual on arrays. We present fully automatic system microarray image quantification. The automatically locates both subarray grids spots, requiring no user identification any coordinates. computed based explicit segmentation each spot. On typical 6000 entire process takes less than 20 sec. quantitative assessment performance multiple replicates genome-wide array-based comparative genomic hybridization experiments. By explicitly identifying pixels spot, yields more accurate estimates ratios assuming spot circularity. software, called UCSF Spot, runs Windows platforms is available free charge academic use.