On Thu, Dec 16, 2010 at 1:27 PM, Wong, Chao-Jen <cwon2@fhcrc.org> wrote:

> 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.
>
>
Yes, I can.  I will need to do things a bit differently than what you
describe below to keep the different result types straight (which is why I
haven't done it yet), but the idea is great.


> 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?
>

See the lumi package....


>
> --------- patch ---------
> cwon2@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')
> 434c434,438
> <   } 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@fhcrc.org
>
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>

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