I am new DESeq2 user, interested in Translation Efficiency (TE) and Log2FoldChange (L2FC) of TE. To the best of my understanding, before DESeq2 calculates TE (RiboSeq/RNASeq), the counts are normalized with the appropriate SizeFactor. The SizeFactors take into account the geometric avg of counts across all conditions.
If the above is correct, then the standalone TE values for each condition are dependent on the counts of other conditions and should not be consistent. Would TPM be a better measure for standalone TE values?