Extending digital PCR analysis by modelling quantification cycle data

Wilson, Philip J.; Ellison, Stephen L. R.

doi:10.1186/s12859-016-1275-3

BMC Bioinformatics

Table 1 Sample means and standard deviations of μ, ν and adjustment factor estimates for simulated data

From: Extending digital PCR analysis by modelling quantification cycle data

μ (molecules/partition)					ν			.5(1 + min(1,E ₁/E))
True value	Count-based mean	C_q-based mean	Count-based s. d.	C_q-based s. d.	True value	C_q-based mean	C_q-based s. d.	True value	C_q-based mean	C_q-based s. d.
0.5	0.487	0.503	0.026	0.023	0.8	0.864	0.171	0.974	0.972	0.010
1.5	1.390	1.501	0.066	0.044	0.8	0.799	0.078	0.974	0.974	0.008
2.5	2.265	2.488	0.110	0.078	0.8	0.823	0.075	0.974	0.995	0.009
3.5	3.118	3.133	0.174	0.308	0.8	1.080	0.163	0.974	0.980	0.070
0.5	0.487	0.502	0.027	0.027	0.8	0.864	0.195	0.895	0.893	0.014
1.5	1.388	1.499	0.064	0.048	0.8	0.806	0.092	0.895	0.895	0.011
2.5	2.270	2.505	0.107	0.081	0.8	0.804	0.083	0.895	0.915	0.020
3.5	3.107	3.053	0.168	0.337	0.8	1.094	0.176	0.895	0.987	0.028
0.5	0.498	0.500	0.027	0.025	1	1.033	0.174	0.974	0.972	0.009
1.5	1.508	1.500	0.064	0.040	1	1.022	0.090	0.974	0.974	0.006
2.5	2.511	2.490	0.122	0.062	1	1.016	0.082	0.974	0.990	0.011
3.5	3.534	3.281	0.232	0.210	1	1.172	0.110	0.974	0.988	0.050
0.5	0.502	0.500	0.031	0.028	1	1.059	0.195	0.895	0.894	0.015
1.5	1.498	1.499	0.069	0.048	1	1.012	0.090	0.895	0.894	0.013
2.5	2.511	2.541	0.120	0.159	1	0.979	0.102	0.895	0.899	0.030
3.5	3.565	3.180	0.237	0.314	1	1.169	0.125	0.895	0.976	0.038
0.5	0.515	0.501	0.030	0.025	1.2	1.222	0.183	0.974	0.973	0.009
1.5	1.613	1.503	0.075	0.043	1.2	1.215	0.088	0.974	0.974	0.008
2.5	2.773	2.496	0.152	0.059	1.2	1.222	0.080	0.974	0.983	0.012
3.5	3.911	3.153	0.243	0.579	1.2	1.296	0.114	0.974	0.978	0.042
0.5	0.510	0.499	0.031	0.026	1.2	1.208	0.167	0.895	0.895	0.013
1.5	1.613	1.523	0.086	0.171	1.2	1.192	0.137	0.895	0.895	0.019
2.5	2.731	2.522	0.125	0.173	1.2	1.174	0.113	0.895	0.896	0.030
3.5	3.961	3.210	0.272	0.449	1.2	1.238	0.135	0.895	0.951	0.050

Sample means and standard deviations of the count-based estimates of μ, using Eq. (1) and the C_q-based estimates of μ, ν and the adjustment factor .5 (1 + min(1,E ₁/E)) from Eq. (6). Each row relates to the estimates for 100 sets of data simulated with E = 0.95 and a different combination of μ, ν and E ₁. E ₁ is either 0.95 (.5(1 + min(1,E ₁/E)) = 0.974) or 0.75 (.5(1 + min(1,E ₁/E)) = 0.895). Boldface is used for the C_q-based means when they are closer to the true values than the count-based means and for the C_q-based s. d.’s when they are smaller than the count-based s. d.’s

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ISSN: 1471-2105

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