Equivavalent of rlog() or vst() for abundance values
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2.4 years ago

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?

RNA-Seq • 660 views