###
###
### The Following are variables that you can change 
### at the very least you should change the first variable
### to something sensible
###
###

dataset.name <- "MyDataSetName"
dir.name <- dataset.name 


## if FALSE use original CEL file names for images (otherwise create
## new file names)
Anonymize <- TRUE       

###
###
### The following code should not need to be modified
###
###

dir.name <- gsub(" ", "", dir.name)

dir.create(dir.name)


library(affyPLM)

My.Data <- ReadAffy()
Pset <- fitPLM(My.Data)


if (Anonymize){
 sampleNames(Pset) <- paste(1:length(sampleNames(Pset)),substr(dataset.name,1,6),sep="-")
}


png(paste(dir.name,"Weights_%03d.png",sep=.Platform$file.sep),height=1024,width=1024,pointsize=18)
image(Pset)
dev.off()

png(paste(dir.name,"Residuals_%03d.png",sep=.Platform$file.sep),height=1024,width=1024,pointsize=18)
image(Pset,type="resids")
dev.off()

png(paste(dir.name,"PositiveResiduals_%03d.png",sep=.Platform$file.sep),height=1024,width=1024,pointsize=18)
image(Pset,type="pos.resids")
dev.off()


png(paste(dir.name,"NegativeResiduals_%03d.png",sep=.Platform$file.sep),height=1024,width=1024,pointsize=18)
image(Pset,type="neg.resids")
dev.off()

png(paste(dir.name,"SignResiduals_%03d.png",sep=.Platform$file.sep),height=1024,width=1024,pointsize=18)
image(Pset,type="sign.resids")
dev.off()


png(paste(dir.name,"NUSE_RLE_%03d.png",sep=.Platform$file.sep),height=1024,width=1280,pointsize=18)
par(las=2)
old.plt <- par()$plt
par(plt=c(old.plt[1],
	old.plt[2],
	0.13,
	old.plt[4]))	
RLE(Pset,names=paste(1:length(sampleNames(Pset)),substr(dataset.name,1,6),sep="-"),col=rainbow(length(sampleNames(Pset))),main=dataset.name,ylab="RLE")
NUSE(Pset,names=paste(1:length(sampleNames(Pset)),substr(dataset.name,1,6),sep="-"),col=rainbow(length(sampleNames(Pset))),main=dataset.name,ylab="NUSE")
dev.off()


sink(paste(dir.name,"Info.txt",sep=.Platform$file.sep))	
sessionInfo()
Pset
sink()