## ----style, eval=TRUE, echo=FALSE, results="asis"------------------------ knitr::opts_chunk$set(message=FALSE, warning=FALSE, error=FALSE, tidy=FALSE) # turn off verbosity BiocStyle:::latex2() ## ----dummy1, include=FALSE----------------------------------------------- ##options(error=recover) options(bitmapType = "cairo") .HaveDummy = !interactive() if(.HaveDummy) pdf("dummy.pdf") ## ----loading, results="hide"--------------------------------------------- library("arrayQualityMetrics") library("ALLMLL") data("MLL.A") ## ----DataPreparation----------------------------------------------------- preparedData = prepdata(expressionset = MLL.A, intgroup = c(), do.logtransform = TRUE) ## ----boxplot, eval=FALSE------------------------------------------------- ## ?aqm.boxplot ## ----metrics------------------------------------------------------------- bo = aqm.boxplot(preparedData) de = aqm.density(preparedData) qm = list("Boxplot" = bo, "Density" = de) ## ----booutliers---------------------------------------------------------- bo@outliers ## ----shortReport--------------------------------------------------------- outdir = tempdir() aqm.writereport(modules = qm, reporttitle = "My example", outdir = outdir, arrayTable = pData(MLL.A)) outdir ## ----dummy2, include=FALSE----------------------------------------------- if(.HaveDummy) dev.off() ## ----pkgs, echo=FALSE, results="asis"------------------------------------ toLatex(sessionInfo())