I have a simple loop of 2-color cDNA microarray experiments containing 6 individuals and 2 technical replicates for each. After batch and printtip normalization I need the intensity values for each feature, for each individual. I ran the following script using lmFit to obtain coefficients for each feature, for each individual: > design <- modelMatrix(targets, ref = "M1") Found unique target names: M1 M2 M3 WB41 WB42 WB45 > design M2 M3 WB41 WB42 WB45 1 0 0 0 -1 0 2 -1 0 0 1 0 3 0 1 -1 0 0 4 0 -1 0 0 1 5 1 0 0 0 -1 6 0 0 1 0 0 > fit <- lmFit(MA.bp, design) Are these coefficients estimates of normalized intensity relative to my arbitrary reference sample? If so, is the coefficient value for my ref 0 or 1? As I used a loop design, not a reference design, I would like to obtain intensity value estimates for all biological replicates. Is there a way to get normalized intensities for all individuals without designating a reference? I tried setting up a design matrix without a reference and got an error when I tried to run lmFit: > uniqueTargets(targets) [1] "M1" "M2" "M3" "WB41" "WB42" "WB45" > design <- uniqueTargets(targets) > design [1] "M1" "M2" "M3" "WB41" "WB42" "WB45" > fitall <- lmFit(MA.bp, design) Error in lmFit(MA.bp, design) : design must be a numeric matrix Thank you. -- Lin Huffman University of Texas, Dept of Integrative Biology