?scran::pairwiseTTests as well as the code on GitHub but could not find out whether the
lfc argument and corresponding output column prefixed with
logFC was log2 or natural log. I assume that it is base 2 as the
Thanks in advance!
It's the same base as the log-transformation that was used to create the
assay.type. If you were following the standard workflow using, e.g.,
scater::normalize, then yes, this would be base 2. If you did your own thing, then it's whatever base you used to compute the input
x. I'll mention this explicitly in the documentation.