Intersection tests for single marker QTL analysis can be more powerful than two marker QTL analysis

Coffman, Cynthia J; Doerge, RW; Wayne, Marta L; McIntyre, Lauren M

doi:10.1186/1471-2156-4-10

BMC Genomic Data

Table 4 Marker analysis for ovariole number in Drosophila melanogaster from analysis using intersection test, α = 0.025, two marker regression test α = 0.05; and interval mapping; only markers significant in either the two marker test or intersection test listed

From: Intersection tests for single marker QTL analysis can be more powerful than two marker QTL analysis

		Two marker test			Intersection test						Interval mapping
Chromosome	Marker	Frequency M₂N₂	M₂N₂ df	M₂N₂ p-value	Frequency M₂	Frequency N₂	M₂ df	N₂ df	M₂ p-value	N₂ p-value	p-value
1	3E-4F	0.67	94	0.029	0.67	0.86	96	95	0.14	0.0256	0.0242
	4F-5D	0.81	93	0.032	0.86	0.84	95	96	0.0256	0.056	0.0226
	6E-7D	0.7	93	0.0499	0.83	0.74	96	95	0.069	0.1	0.0373
2	35B-38A	0.69	82	0.028	0.81	0.83	89	84	0.33	0.017	0.3036
	38A-38E	0.7	77	0.017	0.83	0.88	84	87	0.017	0.028	0.0105
	38E-43A	0.71	78	0.028	0.88	0.84	87	84	0.028	0.038	0.0083
	43A-43E	0.73	79	0.03	0.84	0.9	84	87	0.038	0.034	0.0177
	43E-46C	0.8	85	0.038	0.90	0.89	87	89	0.034	0.073	0.0339
3	63A-65A	0.29	85	0.075	0.49	0.38	94	89	0.227	0.0249	0.0187
	65A-65D	0.3	86	0.035	0.38	0.51	89	93	0.0249	0.13	0.0207
	65D-67D	0.42	90	0.021	0.51	0.51	93	94	0.13	0.004	0.0031
	67D-68B	0.44	91	0.00004	0.51	0.58	94	94	0.004	0	0
	68B-68C	0.46	90	0.00003	0.58	0.49	94	92	0	0.002	0
	68C-69D	0.41	89	0.002	0.49	0.46	92	94	0.002	0.007	0.0013
	69D-70C	0.34	86	0.0007	0.46	0.45	94	90	0.007	0.0008	0.001
	70C-71E	0.35	84	0.0002	0.45	0.38	90	89	0.0008	0.0006	0.0009
	71E-72A	0.35	84	0.0002	0.39	0.42	89	90	0.0006	0.0007	0.0016
	72A-73D	0.39	88	0.0001	0.42	0.46	90	90	0.0007	0.0003	0.001
	73D-76A	0.34	83	0.0001	0.46	0.37	90	87	0.0003	0.0001	0.0007
	76A-76B	0.34	85	0.0001	0.37	0.45	87	92	0.0001	0.0009	0.0005
	76B-77A	0.41	90	0.0008	0.45	0.44	92	92	0.0009	0.0009	0.0009
	77A-82D	0.34	83	0.0002	0.44	0.38	92	87	0.0009	0.0003	0.0011
	82D-85F	0.31	84	0.0006	0.38	0.38	87	90	0.0003	0.0012	0.0006
	85F-87B	0.27	84	0.0019	0.38	0.32	90	89	0.0012	0.003	0.0012
	87B-87E	0.28	85	0.008	0.32	0.34	89	91	0.003	0.01	0.0028
	87E-87F	0.27	84	0.006	0.34	0.30	91	89	0.011	0.004	0.0066
	87F-88E	0.23	85	0.13	0.3	0.32	89	88	0.004	0.11	0.0061
	96A-96F	0.2	87	0.066	0.32	0.27	94	90	0.21	0.013	0.0176
	96F-97D	0.23	86	0.013	0.27	0.36	90	92	0.013	0.048	0.0168
	97D-97E	0.3	88	0.024	0.36	0.32	92	90	0.048	0.02	0.053
	97E-98A	0.26	88	0.013	0.32	0.34	90	94	0.02	0.018	0.016
	98A-99A	0.27	88	0.0001	0.34	0.4	94	90	0.018	0	0.0001
	99A-99B	0.34	88	0	0.40	0.43	90	90	0	0.0000	0
	99B-99E	0.32	88	0	0.43	0.33	90	94	0	0.0000	0
	99E-100A	0.33	93	0	0.33	0.34	94	95	0	0.0000	0

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