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switch(.Platform$OS.type, unix = .libPaths("/net/arrays/Affymetrix/bioconductor/library/"),"windows")
.libPaths("$R_library")
library(affy)
cel.file.name <- c("$cel_file")
output.file.name <- c("$out_R_CHP_file")
data <- ReadAffy(filenames = cel.file.name)
eset <- mas5(data,sc=250)
PACalls <- mas5calls(data,alpha1=0.05,alpha2=0.065)
Matrix <- exprs(eset)
output <- cbind(row.names(Matrix),Matrix,exprs(PACalls),se.exprs(PACalls))
headings <- c("Probesets","MAS5_Signal","MAS5_Detection_calls", "MAS5_Detection_p-value")
write.table(output,file=output.file.name,sep="\\t",col.names = headings,row.names=FALSE)
jpeg("$out_chip_image", width=1000, height=1000)
image( data[,1] )
dev.off()
END
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