I have three groups let's say C, L, and T, each with three replicates. I did comparison between C vs L, C vs T, and L vs T to find the Deferentially expressed genes in each compassion. I used RUVs package to find the DE genes. I want to draw a heatmap of these differentially expressed genes, but I have different set of DE genes in each case. I have following two questions on this:
- What values should I use to generate the heat map? Is it raw counts OR the fitted values after the GLMfit function?
- How to draw the heatmap for if their are different set of genes in each case?