I have RNA-seq data that I would like to visualise with a PCA plot and a heatmap. I am wondering whether I should use normalised or log transformed normalised counts for this.
I have generated TMM-normalised counts per million in EdgeR as follows:
y <- calcNormFactors(y) tmm <- edgeR::cpm(y)
I have also generated log2 transformed normalised TMM CPM:
tmm_log <- edgeR::cpm(y, log = T, prior.count = 1)
I am wondering whether it is best to use just the normalised CPMs, or the log-transformed normalised CPMs for a PCA plot and heatmap. I find that the plots look better when I use log-transformed normalised counts, but I am not sure whether this is the correct approach.
Could someone please explain why you would/would not want to use log counts?