Thank you so much Tim! I'll try this workaround until an "official protocol" comes out for this. Best, Xavi. De: Tim Triche, Jr. [mailto:tim.triche@gmail.com] Enviado el: dilluns, 29 / octubre / 2012 17:34 Para: Sole Acha, Xavi CC: bioconductor@r-project.org; Kasper Hansen; Jovana Maksimovic Asunto: Re: [BioC] CHARM with Illumina 450K 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 <tel:%2b34%2093%20260%2071%2022> / +34 93 260 71 86 <tel:%2b34%2093%20260%2071%2086> (ext. 7122) Fax: +34 93 260 71 88 <tel:%2b34%2093%20260%2071%2088> E-mail: x.sole (at) iconcologia.net [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- A model is a lie that helps you see the truth. Howard Skipper <http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]