Question: Equivavalent of rlog() or vst() for abundance values
3
gravatar for kristoffer.vittingseerup
5 months ago by
European Union
kristoffer.vittingseerup3.0k wrote:

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 • 154 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by kristoffer.vittingseerup3.0k
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