I have used Voom to transform my data with the TMM scaling factor and identified a list of differentially expressed genes for my RNA-seq data. What I want to do next, is to generate a bar plot on some genes of interest and also plot an expression heatmap. My question is, can I use the transformed E values from
Voom for this, or should I recalculate the Log2CPM values using the
cpm(x, log=T, prior.count = 0.5). I had taken a look at the transformed counts from both functions and their differences are subtle. I'm not sure which one is most ideal. Thanks for the help in advance.