DESeq2 documentation states that input needs to be un-normalized counts (=raw counts?),
tximport suggests for salmon data to apply
countsFromAbundance="lengthScaledTPM" and use the result as a regular count matrix.
- To my understanding
tximportimplies that it's length scaled counts can be treated like un-normalized counts in DESeq2. But why? Is it because these bias corrected counts from
tximportare different from normalized or transformed counts?
- Are there any reasons to prefer importing raw read counts (with offset) over
countsFromAbundance="lengthScaledTPM"or can they be used likewise?
- As the outcome of
countsFromAbundance="lengthScaledTPM"is corrected on a similar scale as TPMs: Could I use the data likewise, e.g., to compare counts between different genes within the same sample? And after transformation via rlog/vst would the values be on a scale that could be compared between genes AND between samples? Basically TPM would not be required anymore?
I´m grateful for any clarification.