[BioC] LIMMA contrast matrix help

[Maria Kamarinos]

Hello Everyone

I am working through my data using the LIMMA users guide and have a question 
about forming a contrast matrix using a reference design. I have four samples 
in my experiment (A, B,C and D) which i compared to a common reference using 
dye swaps in a total of eight comparisons. I have generated the following 
design matrix:

	A	B	C	D
1	1	0	0	0
2	-1	0	0	0
3	0	1	0	0
4	0	-1	0	0
5	0	0	1	0
6	0	0	-1	0
7	0	0	0	1
8	0	0	0	-1

The comparisons that i am interested in are between A and B, C and D, B and D. 
When designing my contrast matrix my initial thought was to put the following 
command into LIMMA:

>contrast.matrix<-makeContrasts(A-B,C-D,B-D,levels=design)

My question concerns how the dye swaps are handled in this situation. Should i 
also include B-A, D-C and D-B in the contrast matrix to account for dye swaps 
or is this already done?

Thank-you

Maria 

-- 
Maria Kamarinos, PhD
St Vincent's Institute of Medical Research
9 Princes St., Fitzroy, VIC, 3065
Ph: + 61 3 9288 2566
Fax: + 61 3 9416 2676
Email: mariak at medstv.unimelb.edu.au