I am using a publicly available RNA-seq datasets that were processed as follows:
"Gene expression normalizations were performed using the TMM method (PMID: 20196867), and further normalization was applied by adjusting the expression to gene length. In addition, only the genes and that had reads mapped to them in at least 5% of the samples were kept."
Now, if I had a raw read counts table I could easily follow DESeq/EdgeR/Limma but with a TMM normalized table what method shall I follow and what should be my starting point to induct this table in the workflow.
I am certain some of you must have encountered this problem, could please share your knowledge.
Many thanks in advance.