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Replicate filtering between slides can also significantly improve data quality. Scatterplots showing correlation coefficients (r) for the logarithms of the Cy5/Cy3 ratios for duplicate spots within arrays for three arrays used to analyze independently labeled sets of (a) CaOV3 RNA samples (self-self hybridizations) and (b) PA-1 (Cy5) and CaCO2 (Cy3) RNA samples.
