[BioC] limma Dye Swap question

[Mike Schaffer]

I had a question about how limma handles dye swap experiments.

The way we typically run these experiments is to label an aliquot of a 
test set of (amplified) aRNA with Cy3 and another aliquot of the same 
aRNA with Cy5.  We do the same with the control aRNA and hyb opposite 
dyes on two slides (i.e. slide 1: test Cy5/control Cy 3, slide 2: test 
Cy3/control Cy 5).  In the past we would loess normalize the slides, 
calculate an average log2 ratio for the set, and use 1 number to 
represent the experimental M value from the two slides.

Q: Is there any consideration in limma given to the fact that these two 
slides represent the same original RNA sample and therefore (partially) 
represent a technical replicate?

It appears that limma lumps all of the slides together regardless of 
which slides are supposed to be paired with others.  It seems to me 
that these pairs of slides must be considered independently from other 
biological dye-swap replicates.  Can anyone shed some light on how 
limma handles this?

Thanks in advance.

Mike Schaffer
Ph.D. Candidate
Bioinformatics Program
Boston University