DNA methylation arrays as surrogate measures of cell mixture distribution

Houseman, Eugene Andres; Accomando, William P; Koestler, Devin C; Christensen, Brock C; Marsit, Carmen J; Nelson, Heather H; Wiencke, John K; Kelsey, Karl T

doi:10.1186/1471-2105-13-86

BMC Bioinformatics

Table 6 Simulation Results (Noisy Mixtures, n₁ = 200)

From: DNA methylation arrays as surrogate measures of cell mixture distribution

Strong Alternative I (*θ =* 0)
	Truth	Est	SD	SE ₀	SE ₁	SE ₂	pow(0.05)	pow(0.01)
B Cell	0.0	−0.06	1.39	0.92	1.36	1.34	0.065	0.019
Granulocyte	8.0	7.87	2.02	0.39	2.00	1.99	0.974	0.897
Monocyte	0.0	0.05	1.03	0.42	1.04	1.02	0.049	0.012
NK	0.0	−0.02	1.21	1.02	1.16	1.18	0.061	0.010
T Cell (cd4+)	−4.0	−4.00	1.23	0.79	1.21	1.22	0.903	0.739
T Cell (cd8+)	−2.0	−1.97	1.05	0.80	1.02	0.98	0.517	0.298
Strong Alternative II ( *θ =* 0)
	Truth	Est	SD	SE ₀	SE ₁	SE ₂	pow(0.05)	pow(0.01)
B Cell	0.0	−0.08	1.38	0.92	1.36	1.34	0.063	0.017
Granulocyte	8.0	7.90	2.03	0.39	1.99	1.98	0.973	0.905
Monocyte	0.0	0.10	1.07	0.42	1.04	1.02	0.054	0.019
NK	0.0	0.02	1.17	1.02	1.14	1.18	0.053	0.009
T Cell (cd4+)	−6.0	−5.70	1.19	0.80	1.13	1.16	0.999	0.986
T Cell (cd8+)	0.0	−0.23	1.08	0.81	1.10	1.04	0.066	0.015
Mixed Alternative ( *θ =* 0.5)
	Truth	Est	SD	SE ₀	SE ₁	SE ₂	pow(0.05)	pow(0.01)
B Cell	0.0	0.05	1.42	1.10	1.34	1.34	0.066	0.016
Granulocyte	4.0	4.00	2.01	0.47	2.02	2.01	0.500	0.291
Monocyte	0.0	0.01	1.06	0.51	1.03	1.02	0.072	0.020
NK	0.0	−0.02	1.24	1.22	1.13	1.16	0.064	0.013
T Cell (cd4+)	−2.0	−2.11	1.30	0.95	1.26	1.28	0.391	0.191
T Cell (cd8+)	−1.0	−0.94	1.08	0.96	1.05	1.02	0.163	0.052
Mixed Null ( *θ =* 1)
	Truth	Est	SD	SE ₀	SE ₁	SE ₂	pow(0.05)	pow(0.01)
B Cell	0.0	0.06	1.41	1.59	1.36	1.37	0.062	0.016
Granulocyte	0.0	0.04	2.08	0.67	2.06	2.05	0.056	0.008
Monocyte	0.0	−0.02	1.05	0.73	1.03	1.03	0.058	0.020
NK	0.0	0.01	1.26	1.76	1.14	1.22	0.066	0.011
T Cell (cd4+)	0.0	−0.01	1.42	1.38	1.31	1.36	0.067	0.016
T Cell (cd8+)	0.0	0.00	1.19	1.39	1.08	1.10	0.073	0.011
Strong Null ( *θ =* 0)
	Truth	Est	SD	SE ₀	SE ₁	SE ₂	pow(0.05)	pow(0.01)
B Cell	0.0	0.06	1.37	0.91	1.36	1.32	0.065	0.017
Granulocyte	0.0	0.03	2.07	0.38	2.06	2.05	0.055	0.009
Monocyte	0.0	−0.02	1.04	0.42	1.03	1.02	0.057	0.021
NK	0.0	0.01	1.19	1.01	1.14	1.16	0.053	0.018
T Cell (cd4+)	0.0	−0.04	1.38	0.79	1.31	1.31	0.069	0.015
T Cell (cd8+)	0.0	0.01	1.11	0.79	1.08	1.03	0.065	0.016

Est = Mean regression coefficient estimate (× 100%); SD = SD regression coefficient estimate (× 100%).
SE₀ = Naive standard error (× 100%); SE₁ = Single-bootstrap standard error (× 100%).
SE₂ = Double-bootstrap standard error (× 100%).
pow(α) = Pr{_{P 2} < α}, where P₂ is the p-value computed from SE₂.

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ISSN: 1471-2105

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