Quality control, probe/sample filtering and normalization of Infinium HumanMethylation450 BeadChip data: 'The Leiden Approach'

Here, https://git.lumc.nl/molepi/Leiden450K, we provide a complete workflow for the the preprocessing and analysis of DNA methylation array data. The workflow combines best practices in the field with in-house developed methodology and is geared towards large-scale studies, including Epigenomewide Association Studies (EWAS). A specific aim of the work flow is to support such studies within the BIOS consortium encompassing multiple omics data on 4000 individuals from 6 Dutch biobanks operating within the frame of BBMRI-NL.