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

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