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I wouldn't remove the CpGs. The idea behind DMR identification is to find regions with consistent changes in methylation, and if you select…
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The main purpose for `removeBatchEffect` is to adjust data for nuisance variables prior to plotting (a nuisance variable is meant to contro…
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Yes, your proposed approach is correct. Using arrayWeightsQuick() after an initial lmFit() is suitable for large datasets, providing faster…
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I guess I'd like some further information of the use of covariate within limma for a continuous variable, when there is no batch being corr…
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