I have some RNASeq data, and for the samples, I have counts, normalized counts (RPKM), or variance stabilized counts from DESeq. I have used DESeq on the various conditions to identify differentially expressed genes, and so I also have the baseMean for each condition. It seems you can create a heatmap of the samples using counts, normalized counts, or variance stabilized counts, though the variance stabilized counts are likely are the best.
However, if I wanted to make a heatmap where I summarize the samples into their conditions (treat all biological replicates as one condition), then what are the best values to use? Do I use the baseMean, the mean of the variance stabilized counts, or the mean of the RPKM values?
Because one of the conditions is a control, and all other conditions are being compared to this same control, it is also possible that I might use the fold change, log2 fold change, or the modified log2 fold changes as described by DESeq?