CHARM refers to a custom DNA methylation tiling array design and a normalization pipeline [1, 2]. We currently support data generated using McrBC fractionation and have expanded the list of supported arrays to include several standard Nimblegen designs.
Software features:
- Microarray data quality assessment
- Pre-processing/Normalization
- Probe-level percentage methylation estimates
- Identification of differentially methylated regions (DMRs)
The analysis tools are provided in two forms:
1. The charm R/Bioconductor package
Requirements
- R
- Bioconductor
- The R package charm and its dependencies.
- Raw Nimblegen microarray data (.xys) files.
- RAM: 1Gb + 300Mb/sample (Memory footprint will be reduced in future versions)
This option is recommended for those familiar with R. The charm R package page contains installation instructions and documentation.
2. The charm.jhmi.edu web application
Requirements
- Web browser
- Raw Nimblegen microarray data (.xys) files.
This option requires no local software installation. You use a web browser to upload your raw data, choose analysis options, and view/download results. We recommend starting with the tutorial.
Questions?
aryee |@| jhu edu
References
- Martin J. Aryee, Zhijin Wu, Christine Ladd-Acosta, Brian Herb, Andrew P. Feinberg, Srinivasan Yegnasubramanian, and Rafael A. Irizarry, "Accurate genome-scale percentage DNA methylation estimates from microarray data" (Biostatistics. 2010 Sep 27. PMID 20858772.
- Rafael A. Irizarry, Christine Ladd-Acosta, Benilton Carvalho, Hao Wu, Sheri A. Brandenburg, Jeffrey A. Jeddeloh, Bo Wen, and Andrew P. Feinberg, "Comprehensive high-throughput arrays for relative methylation (CHARM)", Genome Res. 2008 May;18(5):780-90. PMID 18316654.