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Table 2 Optimized parameter values as obtained from the minimization of Eq. (3).

From: Linear model for fast background subtraction in oligonucleotide microarrays

  A. Thaliana C. Elegans D. Melanogaster D. Rerio
GEO no GSE4847 GSE7642 GSE9311 GSE6547 GSE8159 GSE3990 GSE6558 GSE4859
1 0.178 0.196 0.261 0.379 0.520 0.270 0.421 0.338
2 0.050 0.056 0.042 0.047 0.050 0.022 0.025 0.041
3 0.051 0.056 0.041 0.034 0.042 0.024 0.024 0.050
4 -0.013 -0.012 -0.013 -0.012 -0.016 -0.005 -0.011 -0.012
5 -0.013 -0.011 -0.012 -0.010 -0.012 -0.003 -0.010 -0.008
6 0.186 0.198 0.224 0.168 0.271 0.228 0.195 0.140
7 0.004 0.005 0.003 0.003 0.005 0.001 0.005 0.006
8 0.002 0.009 0.003 0.002 0.005 0.001 0.006 0.002
9 0.013 0.027 0.010 0.008 0.008 0.009 0.012 0.014
10 -0.174 -0.192 -0.258 -0.375 -0.517 -0.267 -0.418 -0.334
11 0.063 0.060 0.059 0.058 0.062 0.042 0.057 0.068
12 0.069 0.064 0.064 0.052 0.059 0.046 0.061 0.075
13 -0.017 -0.015 -0.016 -0.011 -0.012 -0.012 -0.013 -0.016
14 -0.018 -0.016 -0.019 -0.010 -0.009 -0.011 -0.014 -0.012
15 0.258 0.299 0.328 0.301 0.459 0.336 0.316 0.246
16 0.004 0.006 0.005 0.005 0.009 0.002 0.008 0.007
17 0.002 0.007 0.003 0.003 0.006 0.001 0.007 0.004
18 0.013 0.025 0.012 0.012 0.015 0.009 0.016 0.016
19 0.068 0.138 0.143 0.149 0.155 0.159 0.217 0.140
20 0.052 0.191 0.169 0.090 0.157 0.124 0.152 0.140
21 -0.021 -0.038 0.006 -0.033 0.030 -0.060 -0.033 -0.069
22 -0.021 0.051 0.056 -0.025 0.072 -0.084 0.003 -0.068
23 -0.032 -0.162 -0.147 -0.038 -0.121 -0.060 -0.094 -0.104
24 0.041 0.075 0.072 0.024 0.015 0.030 0.048 0.035
25 -0.063 -0.221 -0.162 -0.122 -0.140 -0.172 -0.200 -0.190
26 -0.060 -0.130 -0.119 -0.118 -0.109 -0.173 -0.154 -0.181
27 0.000 -0.008 -0.047 0.035 -0.041 0.052 0.035 0.055
28 0.036 0.148 0.076 0.062 0.063 0.105 0.096 0.128
29 -0.026 -0.058 -0.069 -0.046 -0.044 -0.065 -0.085 -0.052
30 -0.050 -0.032 -0.093 -0.065 -0.052 -0.106 -0.102 -0.078
31 0.057 0.037 0.056 0.082 0.012 0.133 0.103 0.130
32 0.093 0.180 0.173 0.125 0.112 0.211 0.181 0.221
33 0.011 -0.074 -0.021 -0.008 -0.026 0.015 -0.036 0.001
34 -0.009 -0.017 -0.016 -0.023 -0.014 -0.035 -0.047 -0.022
Corr. Coeff 0.775 0.686 0.738 0.814 0.700 0.754 0.826 0.705
35 0.020 0.016 0.016 0.019 0.013 0.016 0.012 0.018
36 0.020 0.010 0.012 0.021 0.011 0.016 0.016 0.017
37 0.025 0.025 0.022 0.029 0.019 0.028 0.027 0.031
38 0.024 0.019 0.019 0.028 0.016 0.028 0.023 0.031
39 0.026 0.036 0.034 0.030 0.030 0.027 0.031 0.033
40 0.021 0.021 0.020 0.026 0.021 0.022 0.023 0.026
41 0.028 0.039 0.035 0.036 0.031 0.035 0.038 0.039
42 0.027 0.032 0.031 0.035 0.028 0.033 0.033 0.038
43 0.023 0.024 0.026 0.024 0.023 0.019 0.021 0.021
44 0.020 0.013 0.017 0.022 0.015 0.015 0.017 0.016
45 0.024 0.028 0.028 0.030 0.024 0.027 0.029 0.029
46 0.025 0.025 0.029 0.030 0.024 0.028 0.029 0.030
47 0.020 0.022 0.020 0.022 0.021 0.015 0.019 0.016
48 0.017 0.012 0.012 0.019 0.013 0.010 0.014 0.011
49 0.023 0.029 0.026 0.028 0.023 0.023 0.028 0.026
50 0.023 0.023 0.023 0.028 0.021 0.024 0.026 0.026
Corr coeff -0.679 -0.618 -0.679 -0.759 18 -0.631 -0.683 -0.783 -0.658
  1. Magnitudes and signs of the parameters are approximately constant across different experiments. The correlation coefficients are the Pearson correlations between the nearest-neighbor parameters and the free energy parameters measured in hybridization experiments in aqueous solution [20].