Table 2. Number of CpG % methylation values showing agreement within 5%, 10% and 20% ranges, between Infinium 450K and RRBS (Nreads ≥ 4) data, at different levels of Infinium processing.
| Difference Range (n = 454,660) | within 20% | within 10% | within 5% | Spearman's Rank R | Pearson's R2 | Slope | MIC | |||
|---|---|---|---|---|---|---|---|---|---|---|
|
Probe Type |
Type I |
Type II |
Type I |
Type II |
Type I |
Type II |
|
|
|
|
|
Raw Data |
196,937 |
217,721 |
172,003 |
161,520 |
132,267 |
75,144 |
0.83 |
0.92 |
0.83 |
0.81 |
| 93% |
90% |
81% |
67% |
62% |
31% |
p < 0.001 |
p < 0.001 |
|
|
|
|
After color adjustment |
197,089 |
221,887 |
173,872 |
165,158 |
139,888 |
73,510 |
0.83 |
0.92 |
0.87 |
0.81 |
| 93% |
92% |
82% |
68% |
66% |
30% |
p < 0.001 |
p < 0.001 |
|
|
|
|
After color and Type II adjustment |
197,089 |
225,828 |
173,872 |
192,004 |
139,888 |
144,070 |
0.83 |
0.93 |
0.92 |
0.81 |
| 93% |
93% |
82% |
79% |
68% |
60% |
p < 0.001 |
p < 0.001 |
|
|
|
| After color, Type II and QN |
197,444 |
226,386 |
175,211 |
195,114 |
143,022 |
149,216 |
0.83 |
0.93 |
0.93 |
0.81 |
| 93% | 94% | 82% | 81% | 67% | 62% | p < 0.001 | p < 0.001 | |||
The greatest number of CpGs agreeing at every level, between processing level, are bolded. Overall correlation statistics are also shown (n = 454,660).