Navigating the hydroxymethylome: experimental biases and quality control tools for the tandem OxBS Illumina microarrays. Supplementary data

<b>Table 1.</b> Multivariable
linear regression model outputs for comparing DNA extraction kit performance
between BS and oxBS treated samples, with sample source adjusted.
<b>Table 2.</b> Linear
mixed effect model outputs for comparing DNA extraction kit performance
between BS and oxBS treated samples, with sample source included as a random
intercept.
<b>Table 3.</b> Pairwise
Wilcoxon rank sum test p-values from comparing the internal normalization
control probe (NORM_A/G/C/T) intensities in BS converted and oxBS converted
ccRCC samples.
<b>Figure 1.</b> The probe
call rate difference across all data sets
<b>Figure 2.</b> Principal
component regression analysis of technical variables in ccRCC samples
<b>Figure 3.</b> Coefficient
of variation and ICC in replicate human fetal oligodendrocyte samples.
<b>Figure 4.</b> The recommended 5hmC cut-off batch 1 samples batch 2
samples using <i>oxBSQC</i>.
<b>Figure 5.</b> The distribution of 5hmC signal in low-quality probe
vs high quality probe in batch 1 samples batch 2 samples using <i>oxBSQC</i>.
<b>Figure 6.</b> The CpG genomic location enrichment for low-quality
probes in batch1 and batch2 using <i>oxBSQC</i>.

<b>Figure 7.</b> The distribution of internal normalization
control probe (NORM_A/G/C/T) intensities in BS converted and oxBS converted
ccRCC samples