I have two cell types(11C and 13C) and two groups (KO and CTRL).
sample celltype group
11C-17 11C KO
11C-84 11C KO
11C-C 11C CTRL
13C-17 13C KO
13C-84 13C KO
13C-C 13C CTRL
As shown in the PCA plot, the cell type is the dominant difference. But, I’d like to know whether it’s possible to analyze them together by design matrix design <- model.matrix(~0 + group + celltype) and contrast matrix contrast.matrix <- makeContrasts(KOvsCTRL = KO – CTRL, levels=colnames(design)) to just compare the two groups.
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