A novel model-based intra-array normalisation strategy for 450k data, called BMIQ (Beta MIxture Quantile dilation), to adjust the beta-values of type2 design probes into a statistical distribution characteristic of type1 probes. BMIQ will be useful as a preprocessing step for any study using the Illumina Inﬁnium 450k platform.
Teschendorff, A. E. , Marabita, F. , Lechner, M. , Bartlett, T. , Tegner, J. , & Gomez-Cabrero, D. , et al. 2013. “A beta-mixture quantile normalization method for correcting probe design bias in illumina infinium 450 k dna methylation data.” Bioinformatics, 29(2), 189-196.
R Script for BMIQ This is the script of BMIQ
R Script for DoBMIQ This is a script to run BMIQ on a set of Methylation Data.
To run BMIQ code, after placing all stuffs(data, probe information, annotation) in one folder, you can use following R code to calculate it out:
Or you can find BMIQ function in ChAMP Package, which is developed by Tiffany Morris
Installation To install ChAMP package, start R and enter: