\name{Simulation.pickgene}
\alias{Simulation.pickgene}
\title{Yi Lin's simulations for microarray analysis}
\description{Example simulations}
\usage{
}
\details{}
\keyword{}
\seealso{\cite{multipickgene}}
\examples{
### Note: This uses old pickgene
#detail of the model (7-8). (first run does not include meas error \eta_i)
#par(mfrow=c(3,3))
t<-rnorm(10000,4,2)
changes1<-rep(0,10000)
changes1[1:500]<-rnorm(500)
t1<-t+changes1
changes2<-rep(0,10000)
changes2[1:500]<-rnorm(500)
t2<-t+changes2
s<-rnorm(10000,0,0.1)
cx<-3
cy<-2
t1<-t1+rnorm(10000,0,0.1)
t2<-t2+rnorm(10000,0,0.1)
x<-cx*exp(t1)
y<-cy*exp(t2)
#x<-cx*exp(t1)+rnorm(10000,0,50)
#y<-cy*exp(t2)+rnorm(10000,0,40)
xx<-qnorm(rank(x)/(10000+1))
yy<-qnorm(rank(y)/(10000+1))
#hist(x,breaks=100)
#hist(y,breaks=100)
#plot(x,y)
#hist(y[x<=0],breaks=20)
#hist(x[y<=0],breaks=20)
#plot(xx,yy)
topgenepick<-multipickgene( cbind(xx,yy),condi=0:1,geneID=1:10000, d=1,
                           npickgene=500)$pick[[1]]$probe
abchangesrank<-rank((-1)*abs(t1-t2))
count <- rep(NA,500)
for( i in 1:500 ) {
topipick <- topgenepick[1:i]
count[i] <- sum( abchangesrank[topipick] <= i ) 
}

## Figure 2
plot( 1:500, 1:500, type="n",
     xlab="Rank of 500 most changed genes by our procedure",
     ylab="Number similarly ranked by the 'optimal' procedure",
     xaxs="i", yaxs="i" )
lines( 1:500, count, type="s", lty=1, lwd=2 )
abline(0,1)
\dontrun{dev.print( hor=F, height=6.5, width=6.5, file="rank1.ps" )}

#again, but with the additive noise. (includes \eta_i)
par(mfrow=c(2,2))
t<-rnorm(10000,4,2)
changes1<-rep(0,10000)
changes1[1:500]<-rnorm(500)
t1<-t+changes1
changes2<-rep(0,10000)
changes2[1:500]<-rnorm(500)
t2<-t+changes2
s<-rnorm(10000,0,0.1)
cx<-3
cy<-2
t1<-t1+rnorm(10000,0,0.1)
t2<-t2+rnorm(10000,0,0.1)
### note that noise is very large here (50,40)
x<-cx*exp(t1)+rnorm(10000,0,50)
y<-cy*exp(t2)+rnorm(10000,0,40)
xx<-qnorm(rank(x)/(10000+1))
yy<-qnorm(rank(y)/(10000+1))
hist(x,breaks=100)
hist(y,breaks=100)
plot(x,y,cex=0.4)
#hist(y[x<=0],breaks=20)
#hist(x[y<=0],breaks=20)
plot(xx,yy,cex=0.4)
\dontrun{dev.print( hor=F, height=6.5, width=6.5, file="simudata.ps" )}

topgenepick<-multipickgene(cbind(xx,yy),condi=0:1,geneID=1:10000, d=1,
                           npickgene=500)$pick[[1]]$probe
abchangesrank<-rank((-1)*abs(t1-t2))
count <- rep(NA,500)
for( i in 1:500 ) {
topipick <- topgenepick[1:i]
count[i] <- sum( abchangesrank[topipick] <= i ) 
}
par(mfrow=c(1,1)) # figure 4
plot( 1:500, 1:500, type="n",
     xlab="Rank of 500 most changed genes by our procedure",
     ylab="Number similarly ranked by the 'optimal' procedure",
     xaxs="i", yaxs="i" )
lines( 1:500, count, type="s", lty=1, lwd=2 )
abline(0,1)
\dontrun{dev.print( hor=F, height=6.5, width=6.5, file="rank2.ps" )}

### Figure 5
genepick <- multipickgene( cbind(xx,yy), condi=0:1, geneID=1:10000, d=1)
\dontrun{dev.print( hor=F, height=6.5, width=6.5, file="simutest.ps" )$pick[[1]]$probe}
npick<-length(genepick$pickedgene)
genepick$pickedgene
npick
count[npick]
}