wateRmelon (version 1.16.0)

betaqn-exprmethy450-methods: Calculate normalized betas from exprmethy450 of Illumina 450K methylation arrays

Description

Quantile normalize betas from exprmethy450 objects

Arguments

bn

An exprmethy450 object.

fudge

value added to total intensity to prevent denominators close to zero when calculating betas

Value

exprmethy450 object of the same shape and order as bn.

methods

betaqn( bn ) fuks( bn )

Details

betaqn quantile normalizes betas

References

[1] Pidsley R, Wong CCY, Volta M, Lunnon K, Mill J, Schalkwyk LC: A data-driven approach to preprocessing Illumina 450K methylation array data (submitted)

[2] Dedeurwaerder S, Defrance M, Calonne E, Sotiriou C, Fuks F: Evaluation of the Infinium Methylation 450K technology . Epigenetics 2011, 3(6):771-784.

[3] Touleimat N, Tost J: Complete pipeline for Infinium R Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation. Epigenomics 2012, 4:325-341

[4] Maksimovic J, Gordon L, Oshlack A: SWAN: Subset quantile Within-Array Normalization for Illumina Infinium HumanMethylation450 BeadChips. Genome biology 2012, 13(6):R44