A within array normalization method that substantially reduces the technical variability between the probe types whilst maintaining the important biological differences. The SWAN method makes the assumption that the number of CpGs within the 50 bp probe sequence reflects the underlying biology of the region being interrogated. Hence, the overall distribution of intensities of probes with the same number of CpGs in the probe body should be the same. The method then uses a subset quantile normalization approach to adjust the intensities of the probes on the arrays.

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SWAN classification

SWAN specifications

Software type:
Package
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS, Windows
License:
Artistic License version 2.0
Stability:
Stable
Interface:
Command line interface
Biological technology:
Illumina
Programming languages:
R
Computer skills:
Advanced
Requirements:
methods, BiocGenerics (>= 0.15.3), Biobase (>= 2.17.8), lattice, GenomicRanges, SummarizedExperiment (>= 1.1.6), Biostrings, bumphunter (>= 1.1.9)

Publications

  • (Maksimovic et al., 2012) SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips. Genome biology.
    PMID: 22703947

SWAN support

Documentation

Maintainer

Credits

Institution(s)

Murdoch Childrens Research Institute, Parkville, Australia

Funding source(s)

This work was supported by the Victorian Government's Operational Infrastructure Support Program to MCRI.

Link to literature

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