ENmix

The software tool "ENmix" introduces a novel method called REgression on Logarithm of Internal Control probes (RELIC) to correct for dye bias in Illumina Infinium HumanMethylation450 and MethylationEPIC BeadChip data. These arrays use two fluorescent dyes to measure methylation levels at CpG sites, and performance differences between the dyes can lead to biased estimates. RELIC utilizes intensity values from paired internal control probes monitoring the two color channels to correct for dye bias on the entire array.

Topic

Epigenetics;Microarray experiment;Data quality management

Detail

  • Operation: Data handling;Methylation analysis

  • Software interface: Command-line user interface,Library

  • Language: R

  • License: Artistic License 2.0

  • Cost: Free

  • Version name: 1.38.01

  • Credit: Yhe Center for Environmental Genetics grant (National Institute of Environmental Health Sciences, Intramural Research Program of the NIH, National Institute of Environmental Health Sciences, VITO-FWO post-doctoral fellowship.

  • Input: Microarray hybridisation data [IDAT] [Textual format]

  • Output: Plot [Textual format] [Image format], Report [Textual format] [Image format], Microarray hybridisation data [Textual format] [Image format]

  • Contact: Zongli Xu xuz@niehs.nih.gov

  • Collection: -

  • Maturity: Stable

Publications

  • RELIC: a novel dye-bias correction method for Illumina Methylation BeadChip.
  • Xu Z, et al. RELIC: a novel dye-bias correction method for Illumina Methylation BeadChip. RELIC: a novel dye-bias correction method for Illumina Methylation BeadChip. 2017; 18:4. doi: 10.1186/s12864-016-3426-3
  • https://doi.org/10.1186/s12864-016-3426-3
  • PMID: 28049437
  • PMC: PMC5209853

Download and documentation

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