Dear List,
  It was a lot of discussion recently about paired designs.
  I suppose my question is very simple:
  I have 6 paired arrays (3 pairs, treatment vs control within each pair, 6 arrays in total).
  Could somebody explain briefly if this is correct that two scripts below (with different designs) should produce the same results for paired design in LIMMA(i am getting the same results)? And also, am I creating the design and targets objects correctly?
  1st script:
  >data<-ReadAffy()
  >temp<-rma(data)
  >targets <- readTargets("targets.txt")
  > targets
    FileName Pair Treatment
  1    1.CEL    1         C
  2    2.CEL    1         T
  3    3.CEL    2         C
  4    4.CEL    2         T
  5    5.CEL    3         C
  6    6.CEL    3         T
  >Pair <- factor(targets$Pair)
  >Treat <- factor(targets$Treatment, levels=c("C","T"))
  >design <- model.matrix(~Pair+Treat)
  > design
    (Intercept) Pair2 Pair3 TreatT
  1           1     0     0      0
  2           1     0     0      1
  3           1     1     0      0
  4           1     1     0      1
  5           1     0     1      0
  6           1     0     1      1
  >fit_pair <- lmFit(temp, design)
  >fit_pair <- eBayes(fit_pair)
  >topTable(fit_pair, coef="TreatT")
   
  2nd script:
  >data<-ReadAffy()
  >temp<-rma(data)
  > design2<-cbind(c(1,1,0,0,0,0), c(0,0,1,1,0,0), c(0,0,0,0,1,1), c(0,1,0,1,0,1))
  > colnames(design2)<-c("Pair1", "Pair2", "Pair3", "TreatT")
  > design2
       Pair1 Pair2 Pair3 TreatT
  [1,]     1     0     0      0
  [2,]     1     0     0      1
  [3,]     0     1     0      0
  [4,]     0     1     0      1
  [5,]     0     0     1      0
  [6,]     0     0     1      1
  > fit <- lmFit(temp, design2)
  > fit <- eBayes(fit)
  > topTable(fit, coef=4)
   
  With kind regards,
  Lev.

       
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