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Question about logFC while using DESeq2 in Seurat

Hello, the question I have is - log to which base is reported when we use test.use="DESeq2" in the FindMarkers() function?

I know the default logFC while using Wilcoxon test in FindMarkers() is reported in the natural log, is this true when we use DESeq2 as well? I have this doubt as DESeq2 reports FC in log to the base 2 and not natural log.

Thanks Suvi

rna-seq seurat single-cell deseq2
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written by suvratha • suvratha

2 answers

I'm not sure but the FindMarkers code suggests it only takes the P value from DESeq2 results when you specify test.use="DESeq2".

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written by Arup Ghosh Arup Ghosh

so you mean to say the Log FC reported is natural Log itself like the default?

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written by suvratha • suvratha

Line 552-555 have the code for fold change calculation.

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written by Arup Ghosh Arup Ghosh

Yes but that is only the execution, the function declaration starts at 539.

return(log(x = rowMeans(x = expm1(x = x)) + pseudocount.use)) is the relevant part

with ?log:

log computes logarithms, by default natural logarithms,

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written by ATpoint ATpoint

What makes you say that? This line is part of a function that is not even exported. Not sure for what it is. Any ideas? It is not (at least not based on this script) related to the DESeq2 function of this script.

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written by ATpoint ATpoint

In the last version (v2), everything was done on a natural log scale. See

https://github.com/satijalab/seurat/issues/332

https://github.com/satijalab/seurat/issues/741 (point 1)

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written by Santosh Anand Santosh Anand

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