Hi. I?m trying to look for differentially expressed genes using a saturated design. I have 5 samples which are hybridized in the following scheme. Sample 1 -> sample2, sample3 (sample 1 is hybridized to sample 2 and sample3, sample one is colored by cy5 in both hybridizations and sample 2 and 3 are labelled with cy3) Sample 2 -> sample 3, sample 4 Sample 3 -> sample 4, sample5 Sample 4 -> sample 1, sample 5 Sample 5 -> sample1, sample2 It is easier to visualize if you draw it on a paper, it will look like a pentagram-like structure. The samples are RNA from two cell lines which has been mixed in different proportions, and I would like to see which genes pops up as differentially expressed. I have used the Maanova package from Gary churchill, and I would like to compare the result using the Btest. Do someone know how the design-matrix should be done? Best regards /Marcus