I would also like to bring the attention to another single color platform, beadArray (by Illumina). It sounds less complex (single color), but has more measurements (other than intensity) for each gene (more exactly, oligo reporter): for example, number of beads, and standard deviation of on-the-array technical replicates. We did model it in the lumi package, but we would certainly like to make the design more consistent with other packages. Simon
It is true that option B would require some amount of coding. Martin Morgan and I discussed this a bit we realized that one could have phenoData exactly the same as in option A. The phenoData table would have a special column (label/dye/color/colour) and values would correspond to named matrices in assayData. The eSet extension would then handle subsetting (this is the infrastructure that would need coding). I suspect that the efficiency difference in obtaining an expression matrix for a particular dye will make option B worth the effort. + seth