Which method is most suitable for normalization to BS-seq data between different batches? Is it necessary to do it because each value has been calculated by mCG/umCG in each files?
I assume you're using the raw methylated-CpG and unmethlyated-CpG counts, in which case you can just enter batch into your GLM. If you're actually using a ratio then I haven't a clue how you intend to analyse the results in the first place.
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