A study published in GenomeMedicine suggests a relationship between DNA methylation changes in COVID-19 patients and changes that occur during myeloid differentiation and that can be induced by pro-inflammatory cytokines.
) sites. We used the BS conversion control probe test included in ShinyÉPICo to determine whether the conversion rate was above the quality threshold of 2 established by Illumina. The threshold was calculated from the information of the BS conversion control probes of the EPIC arrays. When the BS conversion reaction is successful, control probes display strong signal in the red channel, whereas if the sample has unconverted DNA, control probes have a strong signal in the green channel.
CpH and SNP loci were removed by the Noob method, followed by quantile normalization. Sex chromosomes were also excluded from the analysis to avoid discordant information among samples. Even when data were generated in a single batch and randomized, we applied the batch effect correction.
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