[BioC] Design matrix: dye-swap or channel-swap?

[John Welsh]

I am confused about the design matrix for gls.series in limma.
I have four two-color microarrays comparing samples A and B.
A is always in channel1 and B is always in channel2.
Red is in the first channel in two of them, and in the other channel in the
other two.

Do I want the design matrix c(-1,1,-1,1) or c(1,1,1,1)?

John Welsh
Associate Professor
Sidney Kimmel Cancer Center
10835 Altman Row
San Diego, CA 92121
(858) 450-5990 ex.282
jwelsh at skcc.org