This comes up a lot, I think Kasper is working on a Real Fix, but...
In the interim, using the example from minfi::preprocessSWAN:

## you will need to be running bioc-devel; otherwise, TSOL
datIlmnSwan <- preprocessSWAN(RGsetEx, mSet = datIlmn)
biocLite("IlluminaHumanMethylation450kannotation.ilmn.v1.2")
SE <- minfi::mapToGenome(datIlmnSwan) ## or coerce from methylumi ;-)

require('charm')
groups <- c(1,1,1,2,2,2) ## I have no idea what's in datIlmn
results <- dmrFinder(eset=NULL, groups=groups,
                                  p=(assays(SE,
withDimnames=F)$Meth)/(assays(SE, withDimnames=F)$Meth+assays(SE,
withDimnames=F)$Unmeth),
                                  chr=as.character(seqnames(SE)),
pos=start(SE), pns=rownames(SE), package='IlluminaHumanMethylation') ##
...more args

cc: Jovana and Kasper in case something is out of whack


On Mon, Oct 29, 2012 at 5:37 AM, Sole Acha, Xavi <x.sole@iconcologia.net>wrote:

> Dear listers,
>
>
>
> I would like to apply the Differential Methylation Region Algorithm (DMRA)
> to a set of Illumina 450K methylation arrays. I have already normalized my
> data using SWAN (package minfi), and now I would like to apply the
> dmrFinder function (charm package) to this normalized dataset. However, the
> dmrFinder function needs an object of class TilingFeatureSet as input, but
> I only have a MethylSet object returned by minfi.
>
>
>
> I would be grateful if anyone could point me about how I could apply this
> method to my 450K normalized dataset.
>
>
>
> Thank you so much for your help in advance.
>
>
>
> Best regards,
>
>
>
> Xavi.
>
>
>
> ------
>
> Xavier Solé Acha
>
> Unitat de Biomarcadors i Susceptibilitat
>
> Unit of Biomarkers and Susceptibility
>
> Institut Català d'Oncologia // Catalan Institute of Oncology
>
> Av. Gran Via de L'Hospitalet 199-203
>
> 08908 L'Hospitalet de Llobregat, Barcelona, Spain.
>
> Phone: +34 93 260 71 22 / +34 93 260 71 86 (ext. 7122)
>
> Fax: +34 93 260 71 88
>
> E-mail: x.sole (at) iconcologia.net
>
>
>
>
>         [[alternative HTML version deleted]]
>
>
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>


-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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