Normalization of methylation EPIC array data before or after subsetting?
Dear all,
I am working on a large DNA methylation dataset (Illumina EPIC array) that comprises 1300 samples from about 900 individuals, with longitudinal measures for 400 individuals. For a differential methylation analysis in a specific subset of this sample (n=600, cross-sectional) I am now wondering which workflow would make more sense:
a) Perform preprocessing and quantile normalization on full dataset, subset afterwards
b) Subset raw data first, perform preprocessing and quantile normalization on subset
For the normalization, minfi::preprocessQuantile() is used.
Is there a recommended way to do this? Thanks for any help!
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In my opinion, it is best practice to normalize all the samples you have together and in differential analysis to use contrasts.