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Experimental evaluation on the specificity of designed arrays with perfect match (PM)/mismatch (MM) probes. One hundred nanograms of genomic DNAs was labeled with Cy3 and hybridized with a modified GeoChip 5.0S in triplicate. For each PM or MM pair, the net signal intensity was obtained by subtracting the signal intensity from the Agilent negative controls within a subarray from the raw signal intensity. The ratio of PM to MM probe pairs was estimated. DvH, D. vulgaris Hildenborough.
