I'm trying to combine the normalized counts of 3 biological replicates into a single column of the normalized count matrix. I need it in order to "absolutely" analyze the expression of specific genes, for example - presenting expressions on heat maps (or other plots) and doing co expression analysis. I would like to emphasize that all 3 biological replicates are, in my point of view, identical, meaning, all are before any treatment, or all of them are after a specific treatment. Yet, I cannot treat them as technical replicates as they were taken from different biological samples. I know that both Deseq2 and EdgeR can collapse technical replicates into a single column, but it is not intended for biological replicates (and I must say that I'm not fully understand why, if all "averaged" replicates represent the same treatment but I'm still a newbie and I accept the verdict). What alternatives do I have? Is it allowed to do a simple average on the normalized counts of each of the 3 samples converting it into a single normalized count?? Any suggestion would be highly appreciated.
Hello marina.rot!
It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/9135173/
This is typically not recommended as it runs the risk of annoying people in both communities.