[BioC] Design Matrix: Dye-swap or channel-swap?

[John Welsh]

Sorry for the formatting error.

Mine is a two color experiment, where each of four chips is a biological
replicate, and half of these are dye-swapped. The (biological) control is
always in the first channel and the treatment is always in the other. My
confusion must stem from the R/G mnenomic: Cy5 fluorescence is in the red
and Cy3 in the green, but this is irrelevant. Limma's R/G refer to false
color. My controls are always false colored red, and the experimentals
always green, irrespective of the dye. Thus, all of the control values
should go into one matrix, and all the experimental values into the other,
and my design would be c(1,1,1,1). Half of the measurements in the R channel
should be cy3 measurements and half should be cy5 measurements. That way,
dye-biased measurements from the same spot, assuming no biological change,
should average out to zero, after normalization. Does that sound right?

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