Hi, Sean and all, I have a couple question. Recently some of the researchers that I are working with are showing interests in using M-value (log ratio of methylation and unmethylation intensities - -log2[(Cy5+1)/(Cy3+1)]) for quantifying methylation levels. A recent paper also indicates that it is a good idea to use M-value methods. Here is the link of the paper: http://www.biomedcentral.com/1471-2105/11/587/abstract I am wondering if you can add the M-value method to the normalizeMethyLumiSet function. Below is the patch that I did to modify MethyLimiSet-class.R in your methylumi package. My second question is that the normalization scheme in the methylumi package is not optimal for Illumina Infinium methylation assay. Does anyone knows what normalization method is suitable for infinium data? --------- patch --------- cwon2 at alpaca:~/proj/Rpacks/methylumi/R> diff MethyLumiSet-class.R MethyLumiSet-class_new.R 391c391 < normalizeMethyLumiSet <- function(x,beta.cuts=c(0.2,0.8),mapfun=c('atan','ratio')) ---
normalizeMethyLumiSet <- function(x,beta.cuts=c(0.2,0.8),mapfun=c('atan','log','ratio'))
432c432
< if(mapfun=='atan') {
---
if(mapfun=='atan')
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< } else {
---
if(mapfun=='log')
newbeta <- log2((cy5+1)/(cy3+1))
if(mapfun=='ratio')
436c440 < } ---
Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M1-B514 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2 at fhcrc.org