[BioC] Normalized Intensities for 2-color arrays in LIMMA

[Lin Huffman]

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