Skip to main content

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.

From: A method for detecting and correcting feature misidentification on expression microarrays

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