Hello List, I am trying to extract estimates of intensity for each sample in a two-color, simple loop design microarray experiment. I need these values to do hierarchical clustering and make heat maps for all samples. I have 2 groups (M and WB), 3 biological replicates in each group, and 2 technical replicates for each sample, totaling 6 hybes. I used a reference design and lmFit: design <- modelMatrix(targets, ref = "M1") 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) write.table(fit, file="lmFit.txt", sep="\t") This output "coefficients" for each sample, for each feature. Are these estimates of intensity? It does not calculate coefficients for the reference sample (M1, in this case). How do I get these values? I have also tried converting the targets file AC format and running intraspotCorrelation, which doesn't work because I have missing values: targets <- targetsA2C(targets) targets u <- unique(targets$Target) f <- factor(targets$Target, levels=u) design <- model.matrix(~0+f) colnames(design) <- u corfit <- intraspotCorrelation(MA.bp, design) Can anyone help me get intensity estimates for all 6 of my samples? Thank you, Lin Huffman -- Lin Huffman lin.winton@mail.utexas.edu linbird@gmail.com University of Texas, Dept of Integrative Biology Hofmann Lab (512) 475-7318 [[alternative HTML version deleted]]