Question

How to compute(calculate) rlog and vst provided from DESeq2

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tstpp • 0

@08250284

Last seen 20 months ago

Japan

I'm not familiar with the calculation of rlog and vst values transformed from count matrix using DESeq2.

Could you tell me the way and process of calculation of rlog and vst using the below count matrix.

Read count matrix

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DESeq2 • 1.0k views

ADD COMMENT • link 21 months ago tstpp • 0

score 1 · Answer 1 · 2023-03-18

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ATpoint ★ 4.6k

@atpoint-13662

Last seen 2 hours ago

Germany

The vst is described in the original DESeq paper (Anders et al). rlog is described in the DESeq2 paper (Love et al). Source code is here https://github.com/mikelove/DESeq2/tree/devel/R and also see ?vst and ?rlog under 'Details`. Read the data into R and run the functions.

ADD COMMENT • link 21 months ago ATpoint ★ 4.6k

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FWIW, you can also search all of Bioconductor code via https://code.bioconductor.org e.g. https://code.bioconductor.org/search/search?q=vst