Hello,
 
 I am using the following code to plot an MVA plot.
 
 library(affy)
 library(Biobase)
 library(limma)
 library(gcrma)
 
     pd<-read.phenoData("Clk.targets.2.txt",header=TRUE,
     row.names=1,as.is=TRUE,sep="\t")
     Data <- ReadAffy(filenames=pData(pd)$FileName,phenoData=pd) 
     Print(Data)
     
     eset <- gcrma(Data) 
     write.exprs(eset, file="clk.6-23-05.txt")
       
         
     bitmap("clk-1.mva.jpg",width=15, height=12)
     mva.pairs(exprs(eset)[,c(19,20,21,22,23,24)],log.it=FALSE)
     dev.off()
 
 but I am getting an subscript out of bound error.
 
 Any Idea ?
 
 Thanks,
 
 Vijay
 
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