I have two-color custom array data, read on genepix.  The design is:

File    Cy3    Cy5
1    unripe1    ripe1
2    unripe2    ripe2
3    ripe1       unripe1
4    ripe2       unripe2

But the custom arrays have three spots for each probe, in an uneven spacing
(e.g. spot 2 - spot 1 = 20 lines, but spot 3 - spot 2 = 32 lines).  I got
around the spacing issue by sorting the genes by name, but I'd like to
account for both the on-chip replicates and the fact that file 1 and file 3
(and file 2 and file 4) are dye swaps of the same two samples ..
*not*biological replicates.  ?duplicateCorrelation says this:

*At this time it is not possible to estimate correlations between duplicate
spots and between technical replicates simultaneously.  If 'block' is not
null, then the function will set 'ndups=1'.*

What are my options (in or outside of limma)?

Thanks in advance for any help,
~Joe




-- 
Joseph Fass
Bioinformatics Programmer
UC Davis Bioinformatics Core
joseph.fass -at- gmail.com (professional)
970.227.5928 (c)  ||  530.752.2698 (w)

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