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.

Not sure what you're asking. The average expression across all samples is what the baseMean column of results() returns. This is simply the rowMeans of the normalized_counts. With normalized_counts you can take means across any group you like.