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SQN.demo.data <- function(){
mu0a=mu0b=rnorm(1000,5,1.8) ## control probes
mu1a=rnorm(5000,5,0.8);mu1b=mu1a+2 ## probes for signal
ya=c(rnorm(1000,mu0a,.3),rnorm(5000,mu1a,.3))
yb=c(rnorm(1000,mu0b,.3),rnorm(5000,mu1b,.3))+1 ## a systematic bias introduced
Y=cbind(ya,yb) #before normalization
Ynorm=SQN(Y,ctrl.id=1:1000) #after normalization
}
## par(mfrow=c(1,2))
## boxplot(Y,main="before normalization")
## boxplot(Y[1:1000,],add=T,col=3,boxwex=.4)
## boxplot(Ynorm,main="after normalization")
## boxplot(Ynorm[1:1000,],add=T,col=3,boxwex=.4)
## legend(1,10,legend=c("probes for signal","negative control probes"),text.col=c(1,3),bg="white")
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