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Table 1 The GP parameters and limits for different filtering conditions in GP.

From: Advanced spot quality analysis in two-colour microarray experiments

   Filtering conditions
  Parameter Strong Medium Weak Standard
1 Dia. >= 120 >= 100 >= 70 NR
2 % > B635+2SD > 98 > 95 > 66 > 55*
3 % > B532+2SD > 98 > 95 > 66 > 55
4 F635% Sat. < 1 < 5 < 10 < 2–3
5 F532% Sat. < 1 < 5 < 10 < 2–3
6 Rgn Ratio (635/532) > 0 > 0 > 0 NR
7 Rgn R2 (635/532) > 0.8 > 0.6 > 0.4 > 0.5
8 Circularity > 85 > 80 > 50 > 80
9 F635 Median – B635 > 600 > 400 > 200 NR
10 F532 Median – B532 > 600 > 400 > 200 NR
11 SNR 635 > 10 > 5 > 2 > 3
12 SNR 532 > 10 > 5 > 2 > 3
13 Flags >= 0 >= 0 >= 0 >= 0
  1. The table summarises the main parameters and limits for different filtering conditions used in GP. Other parameters and limits that are used in default/standard filtering setting of GP/Acuity are: [Sum of Medians (635/532)] > 200–500, [B532 CV] < 25, [B635 CV] < 25, LCase([ID]) <> "empty". NR indicates that a corresponding parameter is not a default parameter as recommended in GP.