At 11:09 PM 30/06/2004, Marcus Gry Bj?rklund wrote: >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? One way would be to create a 'targets' data.frame, as in section 7.3 of the Limma User's Guide, and to use design <- modelMatrix(targets, ref="Sample 1") This would create 4 coefficients comparing each of the other samples to Sample 1. Gordon >Best regards >/Marcus