I need to describe in more detail how the built-in transformation of data of the DESeq2 function normalises raw counts.
Can anyone give me a reference to a paper where this has been described? I have not been able to find anything yet, unfortunately.
If you have questions like that (how does tool x does y), the first step is always to read the paper a tool is based on. That in this case would be Love et al 2014. Searching for "normalization" will get you to the respective paragraph where they reference the original DESeq paper (Anders & Huber 2010) which describes the process in detail. Maybe easier to digest would be the StatQuest video breaking down the process nicely: