Question: What is lfcSE and how is it calculated?
0
gravatar for lizzid
28 days ago by
lizzid0
lizzid0 wrote:

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 • 73 views
ADD COMMENTlink modified 28 days ago • written 28 days ago by lizzid0
Answer: What is lfcShrink and how is it calculated?
0
gravatar for Michael Love
28 days ago by
Michael Love26k
United States
Michael Love26k wrote:

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.

ADD COMMENTlink written 28 days ago by Michael Love26k

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.

ADD REPLYlink written 28 days ago by lizzid0

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

ADD REPLYlink written 28 days ago by Michael Love26k
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