Welcome!

Updated 04/03/2013 by Roderick
Welcome to Non Scientia. The platform I mainly use (next to Epityper) for measuring DNA methylation is the Illumina 450k array. There are that many packages; if you are a beginner you are overwhelmed by the number of packages available. Here I try to give an overview of available packages and latest 450k literature.

450k array design
The analysis of 450 methylation data is complicated by the presence of two types of probes:type I and type II. Type I uses two types of beads that measure the methylated and unmethylated signal separately but within one color channel, either red or green. Type II probes however, use only one bead but two different color channels, red and green for the unmethylated and methylated signal. However, this is where the normalization can help you out: it can make the distributions of the probe types more similar.
 
Full-size image (68 K)
Figure without permission (booo!) adapted from Science Direct. Bibikova et al.  


Annotation packages
Package  Developer  Resource  Features
  IlluminaHumanMethylation450k.db    Tim Triche  Bioconductor - Annotations for Illumina ID >> hg18/19 genome, probe type, control probes
- Several annotations to general UCSC tables including CpG islands, DHSs, enhancers, Entrez IDs
 lluminaHumanMethylation450kmanifest  Kasper Daniel Hansen,
Martin Aryee
 Bioconductor  Manifest for Illumina's 450k array data, as releassed by Illlumina

Other packages
Package  Developer  Resource  Features
   Genomic Features
 M. Carlson
 et al
 Bioconductor Great package with several functions that make life a lot easier:
- FindOverlaps: find overlaps between for example two GRanges objects
- Distance to nearest: Distance to next feature by comparing two for example GRanges objects
- Subsetby: remove a subset from a set of genomic features



























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Epigenomics of Common Diseases 2015

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Portfolio/list of publications.


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