## ---- echo=TRUE---------------------------------------------------------- library(HTqPCR) library(mvtnorm) library(nondetects) data(oncogene2013) ## ---- echo=TRUE---------------------------------------------------------- normCt <- normalizeCtData(oncogene2013, norm = "deltaCt", deltaCt.genes = "Becn1") ## ---- echo=TRUE---------------------------------------------------------- conds <- paste(pData(normCt)$sampleType,pData(normCt)$treatment,sep=":") resids <- matrix(nrow=nrow(normCt), ncol=ncol(normCt)) for(i in 1:nrow(normCt)){ for(j in 1:ncol(normCt)){ ind <- which(conds==conds[j]) resids[i,j] <- exprs(normCt)[i,j]-mean(exprs(normCt)[i,ind]) } } ## ---- echo=TRUE---------------------------------------------------------- iND <- which(featureCategory(normCt)=="Undetermined", arr.ind=TRUE) iD <- which(featureCategory(normCt)!="Undetermined", arr.ind=TRUE) boxes <- list("observed"=-resids[iD], "non-detect"=-resids[iND]) ## ---- echo=TRUE---------------------------------------------------------- boxplot(boxes, main="",ylim=c(-5,5), ylab=expression(paste("-",Delta,"Ct residuals",sep=""))) ## ---- echo=TRUE---------------------------------------------------------- oncogene2013_1 <- qpcrImpute(oncogene2013, groupVars=c("sampleType","treatment"), outform = c("Multy"), vary_fit=FALSE, vary_model=TRUE, add_noise=TRUE, numsam=2, linkglm = c("logit")) ## ---- echo=TRUE---------------------------------------------------------- normCt <- normalizeCtData(oncogene2013_1[[1]], norm = "deltaCt", deltaCt.genes = "Becn1") ## ---- echo=TRUE---------------------------------------------------------- normCt <- normCt[-which(featureNames(normCt)=="Becn1"),] ## ---- echo=TRUE---------------------------------------------------------- conds <- paste(pData(normCt)$sampleType, pData(normCt)$treatment,sep=":") resids <- matrix(nrow=nrow(normCt), ncol=ncol(normCt)) for(i in 1:nrow(normCt)){ for(j in 1:ncol(normCt)){ ind <- which(conds==conds[j]) resids[i,j] <- exprs(normCt)[i,j]-mean(exprs(normCt)[i,ind]) } } ## ---- echo=TRUE---------------------------------------------------------- iI <- which(featureCategory(normCt)=="Imputed", arr.ind=TRUE) iD <- which(featureCategory(normCt)!="Imputed", arr.ind=TRUE) boxes <- list("observed"=-resids[iD], "imputed"=-resids[iI]) ## ---- echo=TRUE---------------------------------------------------------- boxplot(boxes, main="",ylim=c(-5,5), ylab=expression(paste("-",Delta,"Ct residuals",sep=""))) ## ---- echo=TRUE---------------------------------------------------------- library(nondetects) data(sagmb2011) ## ---- echo=TRUE---------------------------------------------------------- library(nondetects) data(nature2008) ## ---- echo=TRUE---------------------------------------------------------- sessionInfo()