How to generate heatmap for three groups

Question

[manish20072013]

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:

1. What values should I use to generate the heat map? Is it raw counts OR the fitted values after the GLMfit function?
2. How to draw the heatmap for if their are different set of genes in each case?

Thanks!