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) [[alternative HTML version deleted]]