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. Author manuscript; available in PMC: 2016 Aug 1.
Published in final edited form as: Epigenomics. 2015 Sep 14;7(5):813–828. doi: 10.2217/epi.15.21

Table 2.

Comparison of 450K data preprocessing methods/algorithms.

Package/
method		 GenomeStudio SQN [21] SWAN [22] Methylumi [25] /
lumi [26]		 BMIQ [24] IMA/peak
adjust [20]
Raw data
processing		 Y N N Y N N
Background/
control		 Y; optional Y N Y NA NA
Color bias
adjustment		 N Y Y Y N N
Design I and II
bias correction		 N Y Y N Y Peak shift
Across sample
normalization		 N or
background
control norm		 Y N Y (Pool/QN) N Optional QN

BMIQ: Beta mixture quantile dilation; IMA: Illumina methylation analyzer; N: No; NA: Not applicable; QN: Quantile normalization; SQN: Subset quantile normalization; SWAN: Subset quantile within array normalization; Y: Yes.