

Hello,

I have become confused about the use of the block argument in the 
lmFit function of limma when dealing with technical replicates.

I have a common reference design with 38 slides (19 cDNAs x 2 replicates).

Previously I used lmFit in this manner:
####################################
 > cor <- duplicateCorrelation(Mmatrix_ny, design=design,
+ 
block=c(1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13,14,14,15,15,16,16,17,17,18,18,19,19)
+ )
  > cor$cor
[1] 0.06795489
 > fit <- lmFit(Mmatrix_ny, design=design, correlation=cor$cor)
####################################
But after re-reading the limma user's guide again I believe the lmFit 
line should read:
####################################
 > fit <- lmFit(Mmatrix_ny, design=design, 
block=c(1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13,14,14,15,15,16,16,17,17,18,18,19,19), 
correlation=cor$cor)
####################################

But I am still uncertain.  Which is correct?

Thanks for your time,  Carolyn


	[[alternative HTML version deleted]]

