How to compute(calculate) rlog and vst provided from DESeq2
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tstpp • 0
@08250284
Last seen 1 day 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.

DESeq2 • 115 views
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ATpoint ★ 2.4k
@atpoint-13662
Last seen 7 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.

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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

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Thank you for your kind reply! I try to understand them.