Hello Biostars I wish to plot a heatmap from a two color microarray data. The experiments used a common reference design and compared tumor samples with paired normal samples. So for one set tumor RNA was labelled with CY5 and reference RNA with CY3. In the next set Normal RNA was labelled with CY5 and reference RNA with CY3. No replicates. Ive used LIMMA, preprocessed, normalized and got a set of genes which are differentially expressed between two groups. I want to plot a heatmap from this data, but I only have a list of genes that are differentially expressed between the two groups. What values should I use for the heatmap. Is it the M values from the MAList? Im following the limma userguide for arriving at the differentially expressed genes but not sure how to plot heatmaps from there. Any help with the theory and the R code will be greatly appreciated.