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Table 1 Mean bias in background estimates. Mean bias for various region-based background estimates, as well as for various quantile and morphological filter estimates. The bias is measured relative to Fixed18,t.mean. The structuring elements for the quantile filter γB,{0.08}ζb,7are B = 60 × 60 and b = 3 × 3. The subscript of Fixed R is the radius of the background circle mask. The size of the morphological filters Spot's morph.close.open and morph.open is the default value (kscale = 2.5, s r = s c = 25).

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 -2.95 -3.52 -3.09 -2.39 -3.76 -2.05 -3.77 -2.70
GenePix Pro -1.53 -1.92 -1.83 -1.19 -1.18 -1.18 -0.13 -1.58
Fixed 35 -2.95 -3.52 -3.10 -2.37 -3.75 -2.05 -3.75 -2.70
γ B,{0.08} ζ b,7 -0.58 -2.29 -0.80 -1.62 0.13 -1.10 1.81 -1.50
morph.close.open -10.37 -7.92 -9.91 -5.80 -12.67 -5.34 -15.60 -6.99
morph.open -144.90 -62.23 -135.77 -47.27 -189.35 -52.86 -247.66 -68.89