[BioC] Limma analysis

[Pete]

Hi all,
I have been using limma now for a couple of weeks, and I think I have pretty
much got the hang of most of it. However, now I want to analyse a slightly
more complex experiment, can anyone give me some guidance as how to deal
with this.
     Firstly the experimental design is as follows, there are four samples
wildtype tissue A, wildtype tissue B, mutant tissue A and mutant tissue B.
Each sample has been compared to eachother in triplicate (inlcuding a dye
swap, and one independant sample). To complicate things further an
additional set of WT A v WT B was also done in triplicate using a different
method.
    The slides are 7.5k oligos spotted in duplicate ( the duplicates are in
the same block 10 rows below the first copy), although there are control
genes which appear more than twice on the arrays. My files are imagene
output files where the cy5 and cy3 are contained in separate files.  Also
the imagene output contains spots which are flagged and would need to be
removed from the analysis (meaning that a particular gene could have none
one or two measurements for it).

What do you think the best strategy to deal with this design is?

Cheers

Pete