Hi everyone,
The DESeq2
documentation states that input needs to be un-normalized counts (=raw counts?),
while tximport
suggests for salmon data to apply countsFromAbundance="lengthScaledTPM"
and use the result as a regular count matrix.
- To my understanding
tximport
implies that it's length scaled counts can be treated like un-normalized counts in DESeq2. But why? Is it because these bias corrected counts fromtximport
are 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.