DESeq2's output normalized

Hi,

Does DESeq2’s ‘Output normalized counts table’ mean typical normalization like TPM/RPKM/FPKM? Or is some other form of normalization computed internally in DESeq2?

Hi Spring,

Based on the Rscript, the function being used is counts(), which is part of the DESeq2 package. The function includes a parameter, normalized, which “indicat[es] whether or not to divide the counts by the size factors or normalization factors before returning (normalization factors always preempt size factors)”
You can find the description here: counts function - RDocumentation

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Dear spring,

DESeq normalizes by calculating a geometric mean and does not follow a typical TPM/RPKM/FPKM normalization. You can read about the normalization here in this post. Maybe the youtube video helps to better understand it.

Have a good day and best wishes,
Florian

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