What is lfcSE and how is it calculated?
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lizzid • 0
@lizzid-22177
Last seen 4.4 years ago

After callings res() in DESeq2, I see a column for lfcSE. I've read in multiple places that this is the standard error the of the log2 fold change and read in other places that it is not. I'm wondering what this column is for and how it is calculated exactly.

deseq2 standarderror • 3.2k views
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@mikelove
Last seen 17 hours ago
United States

Can you provide your exact code? There isn't a res function in DESeq2, and there isn't a column lfcShrink in the results table. I need to know specifically what you are referring to. Note that there is a lot of details about this in the vignette, so that would be a good place for you to start.

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My apologies. I meant that I called the results() function and see a column for lfcSE which is seen in the edit of my post. The vignette says that lfcSE is the standard error of log2foldchange but I'm wondering what samples and variables that are being taken into account when calculating lfcSE.

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As with your question about size factors, SE of beta (LFC) is detailed in our 2014 paper. Please check their first for method details.

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