[BioC] biological reps and dye-swaps and duplicate spots in a common reference design
pinloche at supagro.inra.fr
Wed Nov 12 17:35:45 CET 2008
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
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