Good day everyone,

The lab i am working in is interested in retrieving the average expression of genes across replicates after finishing performing bulk RNA-Seq using deseq2. Apparently, they are used to this information beside the differential expression list results.

Where i am a little confused is whether this would simply be the normalized counts or the results from rlog/vst?

So, for the normalized counts, i have ran:

normalized_counts <- counts(dds, normalized = TRUE). Since, the normalized count provides counts scaled by size or normalization factors, i imagine this is the average expression of each gene in each replicate.

Your guidance is appreciated thank you.