Hi List,
  I have a questions regarding Limma and 2way ANOVA.  I have a data set containing 2 cell lines and a gene knockout.  So in the design file, I have cell1.KO, cell1.WT, cell2.KO and cell2.WT.  I want to get the differentially expressed genes between KO and WT.  Is the contrast (0.5*(cell1.KO-cell1.WT+cell2.KO-cell2.WT)) right?  Is this the same as looking knockout effect in 2way anova? When I take a look at the heatmap, the genes identified seemed to be differentially expressed in either one of the comparison?
   
  Thanks,
   
  Lisa

 		
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