Experimental Design

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In this experiment, RNA was extracted from 4 samples: Sample 1: Cultivar A mock inoculated Sample 2: Cultivar A inoculated Sample 3: Cultivar B inoculated Sample 4: Cultivar B mock inoculated The samples were compared on a set of 4 slides or arrays (depicted as arrows, labelled A1-A4) following a loop design. The samples at the pointed end of the arrows were labelled with Cy5 and the samples at the other end with Cy3 dye.


Linear model: log2 intensity = μ + treatment + cultivar + ε