aqm.R
In arrayQualityMetrics: Quality metrics report for microarray data sets

## ----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())