# Eklund_script02.txt
# 2007-12-05
# Aron Charles Eklund
# http://www.cbs.dtu.dk/suppl/biascorr/
#
# Fig 5   (Freije glioma dendrogram)
#
#  R 2.5.1

library(affy)
library(bias)
library(RColorBrewer)

load('~/aron/chb/data/int/freije.u133a.batch.RData')

## this data set was saved in an older format; need to update
freije.u133a.batch <- updateObject(freije.u133a.batch)

freije.u133a.rma <- rma(freije.u133a.batch)

freije.u133a.bm <- getBiasMetrics(freije.u133a.batch, freije.u133a.rma)


### set up matrix annotating replicates

myPal <- brewer.pal(9, 'Set1')

replication <- rep(NA, 85)
replication[freije.u133a.rma$Linked == 2 & freije.u133a.rma$Details == 'Replicate'] <- myPal[1]
replication[freije.u133a.rma$Linked == 3 & freije.u133a.rma$Details == 'Replicate'] <- myPal[2]

myMat <- cbind(replication)


### generate dendrograms

## clustering using (1 - Pearson correlation) as distance metric
pclust <- function(x) {
  if( inherits(x, 'ExpressionSet')) x <- exprs(x)
  hclust(as.dist(1 - cor(x)))
}

# Fig. 5a. untreated data
freije.u133a.rma.pclust <- pclust(freije.u133a.rma)

# Fig. 5b. bias-corrected data
freije.u133a.rma.bc <- biasCorrection(freije.u133a.rma, freije.u133a.bm)
freije.u133a.rma.bc.pclust <- pclust(freije.u133a.rma.bc)

### create plots

pl01 <- function(x, figlabel, ...) {
  plotDendroCol(as.dendrogram(x),
    colMat = myMat, leaflab = 'none', colSize = 0.25, 
    colGap = 0.1, xlim = c(3, 83), x.lab.adj = 1, 
    colLab = 'replicate', ...)
  mtext(figlabel, adj = -0.06, font = 2, cex = 1.2)
}

pdf('Fig5.pdf', width = 12, height = 5)
  par(las = 1, mar = c(2, 6, 4, 2), mfrow = c(2,1), cex = 0.75)
  pl01(freije.u133a.rma.pclust, 'a')
  pl01(freije.u133a.rma.bc.pclust, 'b')
dev.off()

###