Table 2.

Test for 96 well plate handling error. a) In this table we see that the middle bank of comparisons indicates a discrepancy between data from the first PCR run and the second, at the 96-well plate level. b) A check of the distance matrix results show that the swapped plates are h and i in one case, and n and o in the other. Bold indicates P-value = 0.3, italic indicates P-values between 1.0E-03 and 1.0E-04, while regular font indicates P-values < 1.0E-04.

a)	R_{m, m}
	PCR Round 1 vs 1				PCR Round 1 vs 2				PCR Round 2 vs 2
Plates	A1 v A2	A2 v A3	A3 v A4	A4 v A5	A2 v B1	A3 v B2	A4 v B3	A5 v B4	B1 v B2	B5 v B3	B1 v B4	B5 v B4
{a, a}	1	1	1	1	1	1	1	2	1	1	2	1
{b, b}	1	1	1	1	1	1	1	1	7	1	3	1
{c, c}	1	1	1	1	1	1	1	1	1	1	1	1
{d, d}	2	1	1	1	1	1	5	9	1	1	1	1
{e, e}	1	1	1	1	1	1	1	2	1	1	2	1
{f, f}	1	1	1	1	1	1	1	1	1	1	1	1
{g, g}	3	1	1	1	1	1	1	1	1	2	1	1
{h, h}	1	1	1	1	343	322	408	294	1	1	1	1
{i, i}	2	1	1	1	421	290	402	359	1	1	1	1
{j, j}	1	1	1	1	2	1	1	1	2	1	4	1
{k, k}	1	1	1	1	2	1	1	1	1	1	1	1
{l, l}	1	1	1	1	1	2	1	1	1	1	1	2
{m, m}	1	1	1	1	1	1	1	1	1	1	1	1
{n, n}	1	1	1	1	255	141	20	167	1	1	1	1
{o, o}	1	1	1	1	330	248	357	277	3	1	5	6
{p, p}	1	1	1	1	1	3	1	1	3	2	1	1
{q, q}	1	1	1	1	4	3	3	2	1	1	1	1
{r, r}	1	1	1	1	1	1	1	5	1	1	5	1
{s, s}	3	1	1	1	1	1	1	1	1	1	1	1
{t, t}	1	1	1	1	1	1	1	1	1	1	1	1
{u, u}	1	1	1	1	1	1	1	1	1	1	1	1
{v, v}	1	1	1	1	1	1	7	1	1	1	1	1
{w, w}	2	1	1	1	1	16	1	2	1	1	1	1
b)	A2 v B1			A3 v B2			A4 v B3			A5 v B4
	D_{mm}		D_{mn}	D_{mm}		D_{mn}	D_{mm}		D_{mn}	D_{mm}		D_{mn}
MEAN	0.33		0.97	0.34		0.89	0.44		0.98	0.37		0.96
SD	0.2		0.11	0.2		0.13	0.21		0.11	0.21		0.12
{h, h}	0.99			1.02			1.07			1
{i, i}	1.09			1			1.07			1.06
{h, i}			0.22			0.09			0.33			0.31
{i, h}			0.28			0.07			0.11			0.14
{n, n}	0.98			0.91			0.85			0.92
{o, o}	1.01			1.02			1.07			1.02
{n, o}			0.1			0.51			0.45			0.52
{o, n}			0.04			0.17			0.11			0.05