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 | ||||||||