Entering edit mode
5.2 years ago
Kristoffer Vitting-Seerup
★
4.1k
We have very nice functions like DESeq2::rlog()
, DESeq2:: varianceStabilizingTransformation()
or DESeq2::vst()
to get abundance estimate from count data which is much more usable/reliable than ad hoc transformations like log2(CPM+1)
.
For readers new to this topic note that the author/maintainer of DESeq2 recomends the vst() approach according to this post and that DESeq2::vst()
is a fast wrapper for DESeq2:: varianceStabilizingTransformation()
.
My question is: whether something similar can be done to abundance values (CPM, RPKM, FPKM, TPM etc) for cases were we cannot get the underlying count data?