[BioC] limma contrast matrix interaction effect

[Dario Strbenac]

Hello,

The correct contrast is AB - A - B + Control.

After you get results, you can use interaction.plot and plot the expression of the top few genes, to see that there is an interaction. Genes which are affected by the interaction of two treatments will have lines that are not parallel.

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Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia