# Kalibrierung und Normalisierung von cDNA Array (R Befehle)

# Zu 1)

library("marrayNorm", verbose=FALSE)
library("marrayPlots", verbose=FALSE)


# Zu 2)

data(swirl)
?swirl
swirl
class(swirl)
getClassDef("marrayRaw")
dim(swirl@maGf)
swirl@maGf


# Zu 3)

# Boxplots of pre-normalization log-ratios for each array in swirl
maBoxplot(swirl, main="Swirl arrays: pre-normalization log-ratios M")

# Boxplots of pre-normalization log-ratios M for each of the 16 
# print-tip-groups 
# - Default arguments
par(mfrow=c(2,2))
for(i in 1:4)
  maBoxplot(swirl[,i])   
par(mfrow=c(1,1))


# MA Plots
par(mfrow=c(2,2))
for(i in 1:4)
  maPlot(swirl[,i])   
par(mfrow=c(1,1))
mtext("Swirl arrays: pre-normalization MA-plot, lowess fits within print-tip-group",line=3)


# Zu 4)

?maNorm
swirl.norm <- maNorm(swirl, norm="median")


# Zu 5)

# Boxplots
par(mfrow=c(1,2))
maBoxplot(swirl, main="Swirl arrays: pre-normalization log-ratios M")
maBoxplot(swirl.norm, main="Swirl arrays: post-normalization log-ratios M")
par(mfrow=c(1,1))

par(mfrow=c(2,2))
for(i in 1:4)
  maBoxplot(swirl.norm[,i])   
par(mfrow=c(1,1))


# MA Plots
par(mfrow=c(2,2))
for(i in 1:4)
  maPlot(swirl.norm[,i])   
par(mfrow=c(1,1))
mtext("Swirl arrays: post-normalization MA-plot, lowess fits within print-tip-group",line=3)


# Zu 6)

swirl.norm <- maNorm(swirl, norm="loess")


# Zu 7) 

library(vsn)
vsn.out <- vsn(swirl[2000:5000,])
dim(exprs(vsn.out))


# Zu 8)

vsn.out@description@preprocessing$vsnParams
vsnPlotPar(vsn.out, "offsets")
vsnPlotPar(vsn.out, "factors")