I am trying to process the raw data downloaded from: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-380 At the moment of using the function neqc I get the following error: Error in if (sigma <= 0) stop("sigma must be positive") : missing value where TRUE/FALSE needed The problem seems to be in this line: In sqrt(weighted.mean(v, freq) * n/(n - 1)) of the function normexp.fit.detection.p This is generated by the fact that in this function, the difference among p-values is computed, and some of those differences turn out to be negative. Following is the code with which I am trying to process the data. library(rstudio) library(beadarray) library(limma) sample.name <- strsplit(dir("~/Workspaces/data/E-MTAB-380/E-MTAB-380.raw.1/"), ".txt") group <- sapplysample.name, function(x) ifelse(length(grep("RR",x))>0,"MT","WT")) setwd("~/Workspaces/data/E-MTAB-380/E-MTAB-380.raw.1/") maqc <- read.ilmn(files=dir("~/Workspaces/data/E-MTAB-380/E-MTAB-380.raw.1/"), probeid = "Reporter name", other.columns = c("Detection", "Avg_NBEADS")) colnames(maqc$E) <- sample.name colnames(maqc$other$Detection) <- sample.name colnames(maqc$other$Avg_NBEADS) <- sample.name maqc$targets <- unlistsample.name) maqc.norm <- neqc(maqc, detection.p='Detection') How can I overcome this?