User: lizzid

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lizzid0
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Posts by lizzid

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Comment: C: What is lfcSE and how is it calculated?
... 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. ...
written 28 days ago by lizzid0
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What is lfcSE and how is it calculated?
... 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 written 28 days ago by lizzid0
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Comment: C: What are size factors used for in baseMean calculation
... So the raw counts are then divided by the sizing factor? ...
written 29 days ago by lizzid0
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What are size factors used for in baseMean calculation
... I am aware that baseMean is the mean of normalized counts and that normalized counts are calculated by: 1. Taking the mean of a gene across samples 2. Dividing each gene sample by the mean 3. Defining the size factor as the median of the genes divided by the mean But what exactly is the size factor ...
deseq2 written 29 days ago by lizzid0 • updated 29 days ago by Michael Love26k

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