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Large studies can be particularly susceptible to the effects of unwanted technical variation due to the large number of samples requiring processing. For example, processing may have to occur over several days or be performed by multiple researchers thus increasing the likelihood of technical differences between ‘batches’. Furthermore, unwanted technical variation is often present against a background of unwanted biological variation.
(Maksimovic et al., 2015) Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data. Nucleic Acids Res.