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 5 Simulation Results (Precise Mixtures, n₁ = 200)

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

Strong Alternative I (*θ =* 0)
	Truth	Est	SD	SE₀	SE₁	SE₂	pow(0.05)	pow(0.01)
B Cell	0.0	0.07	1.00	0.92	0.97	0.98	0.057	0.018
Granulocyte	8.0	8.02	0.73	0.39	0.73	0.73	1.000	1.000
Monocyte	0.0	0.01	0.48	0.43	0.47	0.47	0.055	0.013
NK	0.0	−0.09	1.08	1.02	1.02	1.05	0.066	0.015
T Cell (cd4+)	−4.0	−4.06	0.81	0.80	0.78	0.81	0.999	0.989
T Cell (cd8+)	−2.0	−1.93	0.83	0.81	0.78	0.81	0.653	0.419
Strong Alternative II ( *θ =* 0)
	Truth	Est	SD	SE ₀	SE ₁	SE ₂	pow(0.05)	pow(0.01)
B Cell	0.0	0.00	0.97	0.92	0.97	0.99	0.048	0.016
Granulocyte	8.0	8.00	0.71	0.39	0.72	0.72	1.000	1.000
Monocyte	0.0	0.03	0.48	0.42	0.47	0.47	0.063	0.016
NK	0.0	0.03	1.04	1.02	1.01	1.05	0.052	0.014
T Cell (cd4+)	−6.0	−5.83	0.76	0.80	0.77	0.80	1.000	1.000
T Cell (cd8+)	0.0	−0.22	0.81	0.81	0.80	0.81	0.064	0.014
Mixed Alternative ( *θ =* 0.5)
	Truth	Est	SD	SE ₀	SE ₁	SE ₂	pow(0.05)	pow(0.01)
B Cell	0.0	−0.02	1.02	1.10	0.96	0.98	0.065	0.011
Granulocyte	4.0	3.99	0.75	0.47	0.73	0.73	1.000	0.995
Monocyte	0.0	0.02	0.49	0.51	0.47	0.47	0.060	0.015
NK	0.0	0.04	1.05	1.22	1.01	1.04	0.054	0.009
T Cell (cd4+)	−2.0	−2.07	0.82	0.96	0.79	0.83	0.695	0.471
T Cell (cd8+)	−1.0	−0.95	0.82	0.96	0.78	0.82	0.203	0.082
Mixed Null ( *θ =* 1)
	Truth	Est	SD	SE ₀	SE ₁	SE ₂	pow(0.05)	pow(0.01)
B Cell	0.0	0.00	1.04	1.58	0.96	1.02	0.066	0.017
Granulocyte	0.0	0.03	0.73	0.67	0.74	0.74	0.055	0.014
Monocyte	0.0	−0.01	0.47	0.73	0.47	0.48	0.054	0.013
NK	0.0	−0.01	1.12	1.76	1.01	1.09	0.063	0.014
T Cell (cd4+)	0.0	0.01	0.87	1.38	0.80	0.90	0.054	0.013
T Cell (cd8+)	0.0	−0.02	0.88	1.39	0.79	0.89	0.057	0.015
Strong Null ( *θ =* 0)
	Truth	Est	SD	SE ₀	SE ₁	SE ₂	pow(0.05)	pow(0.01)
B Cell	0.0	−0.01	0.99	0.90	0.96	0.96	0.068	0.014
Granulocyte	0.0	0.03	0.72	0.38	0.74	0.73	0.052	0.013
Monocyte	0.0	−0.01	0.47	0.42	0.47	0.47	0.055	0.013
NK	0.0	−0.01	1.06	1.00	1.01	1.02	0.059	0.020
T Cell (cd4+)	0.0	0.00	0.81	0.78	0.80	0.82	0.054	0.013
T Cell (cd8+)	0.0	−0.01	0.81	0.79	0.79	0.80	0.054	0.015

Est = Men 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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