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To monitor the quality of Illumina 450k data, the array contains 10 different types of quality control probes to evaluate the performance of both samples and specific steps in the process. The most frequently used type of quality control probe is the negative control that represents the background signal level. These are used to determine whether a signal significantly exceeds the background signal (represented as a so-called detection P≤ 0.01 or ≤ 0.05).
(van Iterson et al., 2014) MethylAid: visual and interactive quality control of large Illumina 450k datasets. Bioinformatics.