[BioC] limma_design_matrix.

Marcus Gry Björklund marcusgb at kth.se
Wed Jun 30 15:09:57 CEST 2004


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

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