Linear model for fast background subtraction in oligonucleotide microarrays

Kroll, K Myriam; Barkema, Gerard T; Carlon, Enrico

doi:10.1186/1748-7188-4-15

Algorithms for Molecular Biology

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

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].

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ISSN: 1748-7188

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