## ----style, eval=TRUE, echo=FALSE, results="asis"------------------------ knitr::opts_chunk$set(message=FALSE, warning=FALSE, error=FALSE, tidy=FALSE) # turn off verbosity BiocStyle:::latex2() ## ----options, include=FALSE---------------------------------------------- ##options(error = recover, warn = 2) options(bitmapType = "cairo") ## ----DataLoading--------------------------------------------------------- library("ALLMLL") data("MLL.A") ## ----AffyBatchQM, results="hide"----------------------------------------- library("arrayQualityMetrics") arrayQualityMetrics(expressionset = MLL.A[, 1:5], outdir = "Report_for_MLL_A", force = TRUE, do.logtransform = TRUE) ## ----Normalisation, results="hide"--------------------------------------- nMLL = rma(MLL.A) ## ----ExpressionSet------------------------------------------------------- arrayQualityMetrics(expressionset = nMLL, outdir = "Report_for_nMLL", force = TRUE) ## ----NChannelSet1, results="hide"---------------------------------------- library("vsn") library("CCl4") data("CCl4") nCCl4 = justvsn(CCl4, subsample = 15000) arrayQualityMetrics(expressionset = nCCl4, outdir = "Report_for_nCCl4", force = TRUE) ## ----intgroup1----------------------------------------------------------- pData(nMLL)$condition = rep(letters[1:4], times = 5) pData(nMLL)$batch = rep(paste(1:4), each = 5) ## ----intgroup2----------------------------------------------------------- arrayQualityMetrics(expressionset = nMLL, outdir = "Report_for_nMLL_with_factors", force = TRUE, intgroup = c("condition", "batch")) ## ----XYcoordinates------------------------------------------------------- featureData(nCCl4)$X = featureData(nCCl4)$Row featureData(nCCl4)$Y = featureData(nCCl4)$Column ## ----hasTarget----------------------------------------------------------- featureData(nCCl4)$hasTarget = (regexpr("^NM", featureData(nCCl4)$Name) > 0) table(featureData(nCCl4)$hasTarget) ## ----pData--------------------------------------------------------------- pd = pData(CCl4) rownames(pd) = NULL pd ## ----RIN----------------------------------------------------------------- RIN = with(pd, ifelse( Cy3=="CCl4", RIN.Cy3, RIN.Cy5)) fRIN = factor(RIN) levels(fRIN) = c("poor", "medium", "good") pData(nCCl4)$"RNA-integrity" = fRIN ## ----NChannelSet2-------------------------------------------------------- arrayQualityMetrics(expressionset = nCCl4, outdir = "Report_for_nCCl4_with_RIN", force = TRUE, intgroup = "RNA-integrity") ## ----pkgs, echo=FALSE, results="asis"------------------------------------ toLatex(sessionInfo())