Equivavalent of rlog() or vst() for abundance values
0
3
Entering edit mode
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
ADD COMMENT

Login before adding your answer.

Traffic: 1833 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6