Dear group, I am trying to perform Charm analysis on a dataset consisted of 24 two channel NimbleGen Promoter Medip Arrays. Our data represent same patients' methylation levels before and after treatment so it is a paired design. My problem is, getting an error which I don't understand and don't know how to solve. >setwd("~/Desktop/mydata") >dataDir<-getwd() > pd<-read.delim(file.path(dataDir,"phenoData.txt")) > rawData<-readCharm(files=pd$filename, path=dataDir, sampleKey=pd) > ctrlIdx<-getControlIndex(rawData,subject=Hsapiens) > pData(rawData)$pair=c(1,2,7,4,2,6,3,3,4,5,5,1,7,10,9,9,10,6,8,11,11,8, 12,12) > p<- methp(rawData, controlIndex=ctrlIdx, plotDensity="density.pdf", plotDensityGroups=grp) Spatial normalization Background removal Error in density.default(x, kernel = "epanechnikov", n = n.pts, na.rm = TRUE) : need at least 2 points to select a bandwidth automatically I am running the analysis on a "x86_64-apple-darwin10.8.0" and R version 3.0.0 Is it related to big data size? How can I solve this? Thank you in advance, Zeynep Ozkeserli Ankara University Biotechnology Institute [[alternative HTML version deleted]]