| Â | Infinium I | Infinium II |
|---|
Category | Unique probes | Median | Pearson corr. | P-value | Unique probes | Median | Pearson corr. | P-value |
|---|
High quality | 25,199 | 0.06 | 0.95 | NA | 83,565 | 0.10 | 0.92 | NA |
Multimap map | 917 | 0.08 | 0.93 | 3.43e-09 | 2,602 | 0.11 | 0.91 | 3.72e-03 |
Repeats | 1,645 | 0.13 | 0.85 | 6.1e-141 | 11,026\ | 0.11 | 0.79 | 9.03e-11 |
Indels | 901 | 0.07 | 0.94 | 6.49e-02 | 2,993 | 0.10 | 0.91 | 8.32e-02 |
Bis-okay | 2,734 | 0.07 | 0.95 | 7.74e-02 | 11,804 | 0.10 | 0.92 | 8.32e-02 |
SNP-at-CpG-C | 1,074 | 0.09 | 0.93 | 7.07e-18 | 8,099 | 0.10 | 0.83 | 6.59e-05 |
SNP-at-CpG-G | 1032 | 0.09 | 0.91 | 2.38e-21 | 7,488 | 0.10 | 0.82 | 2.42e-04 |
SNP-1 | 14,155 | 0.07 | 0.95 | 6.33e-12 | 40,426 | 0.10 | 0.91 | 2.30e-01 |
SNP > =2 | 7,067 | 0.07 | 0.94 | 2.36e-27 | 13,822 | 0.10 | 0.90 | 2.27e-01 |
- Each probe count is the number of probes unique to each category and contains only probes which appear on the array and have a matching WGBS beta value. Category definitions: High-quality - contains probes which are not affected by any genomic factors; Repeats - describes probes which hybridize to repetitive regions; Bis-okay – are probes which hybridize regions containing any C- > T SNP or T- > C SNP and are ‘ okay’ in bisulfite space; SNP-at-CpG-C and SNP-at-CpG-G - are probes which have SNPs at the interrogated C and its neighbouring G position, respectively; Indels - are probes which hybridize regions containing INDELs; Multimap - are probes which hybridize to multiple genomic loci; SNP-1 - are probes which contain only a single SNP anywhere in the body; and SNP > =2 - are probes which contain at least 2 SNPs anywhere in the probe body.The p-values represent the difference in beta-value distribution calculated using the Wilcox-rank sum test [39] and multiple tested corrected using the Benjamini-Hochberg method [40]. The median of the absolute difference between WGBS and HM450K bead array of each set is also shown.
