The main input file format to minfi is IDAT files, see read.450k.exp as well as the vignette On Fri, Feb 17, 2012 at 8:40 PM, Tim Triche, Jr. <tim.triche at="" gmail.com=""> wrote: > Obtaining an NChannelSet from the IDATs is not hard (IIRC, minfi will > happily do this as well): > > R> NCh = methylumi:::DFsToNChannelSet(IDATsToDFs(barcodes, idatPath='.')) > > But there don't seem to be any coercion methods for turning it into an > RGChannelSet: > > R> library(minfi) > R> RGset <- as(NCh, 'RGChannelSet') > Error in as(NCh, "RGChannelSet") : > ?no method or default for coercing "NChannelSet" to "RGChannelSet" > > I would think that coercing a MethyLumiSet to a MethylSet would actually be > more productive for using dmr/dmpFinder, etc. ? If it is not obnoxious I > will look into adding a coercion for MethyLumiM/MethyLumiSets to > MethylSets; I recently added one for coercing a MethyLumiSet into a GenoSet > (nice plotting and subsetting functions) and a SummarizedExperiment (same > reasons). > > > > On Fri, Feb 17, 2012 at 11:14 AM, Aaron Mackey <amackey at="" virginia.edu=""> wrote: > >> I'm using the methylumIDAT() function from the methylumi package to read >> data directly from raw .idat files (it was not clear to me whether this >> functionality exists in the minfi package); but I'd like to be able to use >> this object in minfi functions (e.g. controlStripPlot, dmpFinder, etc.), >> but minfi expects RGChannelSet objects, not MethylLumiSet objects. ?Is >> there a way to cast one into the other? >> >> >> Thanks again, >> -Aaron >> >> ? ? ? ?[[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor