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 | ||||
|---|---|---|---|---|---|---|---|---|
| Â | 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 |