[BioC] biological reps and dye-swaps and duplicate spots in a common reference design

[sylvie pinloche]

Hello !

I am comparing the transcriptome of two yeast strains, A and B. For each 
strain we have 5 biological replicates.
The strains are compared to a reference on two-color arrays. For each 
biological replicate, we used two slides, in dye-swap.
So we have 20 slides :

slide    Cy3    Cy5
1        A1      ref
2        ref      A1
3        A2      ref
4        ref      A2
5        A3      ref
6        ref      A3
7        A4      ref
8        ref      A4
9        A5      ref
10      ref      A5
11      B1      ref
12      ref      B1
13      B2      ref
14      ref      B2
15      B3      ref
16      ref      B3
17      B4      ref
18      ref      B4
19      B5     ref
20      ref      B5

In addition, the spots are duplicated on each slide.
So we have biological replicates, technical replicates (dye-swaps) and 
spot duplication. We are interested in genes differentially expressed 
between both strains.
I carefully read the Limma User's Guide, but it seems that it's not 
possible to handle duplicated spots and technical replicates 
simultaneously. In addition I'm not sure how to design my contrast 
matrix for this combination of biological and technical replicates in a 
common reference design...
I would appreciate any help, thank you !

Sylvie Pinloche - INRA