## ----style, eval=TRUE, echo=FALSE, results="asis"------------------------
knitr::opts_chunk$set(message=FALSE, warning=FALSE, error=FALSE, tidy=FALSE) # turn off verbosity
BiocStyle::latex()


## ----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())