[BioC] Limma design and contrast matrix question.

[Dario Strbenac]

Hello,

Your design matrix is correct in the group means style. It is not the only correct way to do it, though.

How you tested for the interaction effect of the two treatments is wrong. The contrast should be Group1 - Group2 - Group3 + Control. I also don't think your Group1 - Control, Group3 - Group1 and Group2 - Group1 contrasts are meaningful.

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Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia