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


## ----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())