Dear Gordon and List,
   
  Thank you very much for your previous e-mails and sorry to bother you with this again.
  Could you please have a quick look at my code (below) for the analysis of AB1700 data where I am trying to get an AveExpr column to be able to create MA plots with the plotMA function?
  My DATA.txt is the matrix with 16 columns, the 1st one represents probe IDs and the other 15 represent raw absolute expression signals for 3 treatments (5 arrays each).
  I would be very grateful if you could let me know whether I am getting things right.
   
  Thank you very much!
  With kind regards,
  Lev.
   
  s<-scan("DATA.txt”, what='character')
  sm<-matrix(s,byrow=TRUE,ncol=16)
  rownames(sm)<-sm[,1]
  sm<-sm[,2:ncol(sm)]
  snn<-apply(sm,2,as.numeric)
  rownames(snn)<-rownames(sm)
  signals<-snn
   
  temp<-normalizeBetweenArrays(log2(signals), method=”quantile”)
   
  design <- model.matrix(~0 +factor(c(1,1,2,2,2,3,2,3,3,3,3,1,2,1,1)))
   
  colnames(design) <- c("Untreated","L1","L2")
  contrast.matrix <- makeContrasts(L1-Untreated, L2-Untreated, L2-L1, levels=design)
   
  library(Biobase)
y <- new("ExpressionSet",exprs=temp)
fit <- lmFit(y,design)
  fit2 <- contrasts.fit(fit, contrast.matrix)
  fit2 <- eBayes(fit2)
  plotMA(fit2, array=1)
  plotMA(fit2, array=2)
  plotMA(fit2, array=3)

       
---------------------------------

	[[alternative HTML version deleted]]

