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Table 2 Squared nearest neighbor deviation measured spot by spot. Comparison of variability in background estimates for region-based methods as well as quantile and morphological filters. The same parameter settings as in Table 1 have been used. By measuring spot by spot the effect of the block structure in the morphological filtered image is reduced, cf. Table 3.

From: Microarray image analysis: background estimation using quantile and morphological filters

Method Slide 1 Slide 2 Slide 3 Slide 4
  green red green red green red green red
Fixed 18 16.05 7.69 17.79 3.98 30.25 2.69 75.40 4.64
GenePix Pro 63.86 44.49 57.80 24.21 139.73 14.27 293.81 22.97
Fixed 35 5.66 3.57 6.80 1.53 12.35 0.95 33.98 1.54
γ B,{0.08} ζ b,7 3.93 2.82 4.98 0.98 9.12 0.68 26.12 1.01
morph.close.open 19.31 7.10 20.19 3.22 38.55 3.25 84.54 5.38
morph.open 25.91 3.45 21.33 1.37 48.30 1.70 103.60 2.81