Unlog transformed data in DESeq2
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@mohammedtoufiq91-17679
Last seen 5 days ago
United States

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 • 1.9k views
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@mikelove
Last seen 16 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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Dear Michael Love, I want to pass RUVIII corrected nanostring data to Deseq2. But it seems that the output (batch normalize count) I am getting from RUVIII is log-transformed. Do you have any suggestions, since we can't pass back-transformed counts to Deseq2 (if I am right)? Thanks. Also wondering if this count is suitable input for limma without any further modification Gordon Smyth thanks.

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The RUVIII people themselves use limma ( https://doi.org/10.1093/nar/gkz433 ). But please, post your question as a question. That would be better than commenting on a comment from an unrelated question from two years ago.

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