Unlog transformed data in DESeq2
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@mohammedtoufiq91-17679
Last seen 1 day ago
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Hi,

I am using DESeq2 for analyzing Illumina RNASeq datasets. I follow the below steps;

  1. Derived raw counts (from featureCounts) > Imported counts to DESeq2
  2. Normalised the counts via an estimation of size factors (counts(dds, normalized = TRUE))
  3. Transformed the data for downstream applications via variance stabilisation (vst) or regularised log (rlog)
vsd <- vst(dds, blind=FALSE)
rld <- rlog(dds, blind=FALSE)
ntd <- normTransform(dds). # this gives log2(n + 1)

My question is if I would like to reverse transform the data in the unlog form - for ntd I would use; dat_unlog = 2^(ntd - 1)

However, If I am interested to unlog the data - from vst or rlog Is it right to use or are there any additional parameters or arguments?

dat_unlog = 2^vst

(OR)

dat_unlog = 2^rlog

Thank you,

Toufiq

RNASeq DESeq2 vst rlog Normalization • 189 views
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@mikelove
Last seen 4 hours ago
United States

All three of these give log2 transform so yes 2^x puts it back on the original scale (but with the sequencing depth variation removed).

Just as a note, don't provide those back-transformed counts to DESeq().

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Dear Michael Love noted and thank you very much for the prompt response. This was helpful.

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