Deseq: What does "BaseMean" mean?
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183227851 • 0
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Deseq: What does BaseMean (output of deseq) mean? I cannot find its description in the manual.
deseq2 • 21k views
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Thanks! If a lot of differential taxa between compared groups were found by Deseq based on the microbiota data, is it necessary to set a cutoff for Basemean to keep more "prevalent" taxa as setting cutoffs for p value and FDR? If necessary, what is generally acceptable cuoff for Basemean?

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Guido Hooiveld ★ 3.9k
@guido-hooiveld-2020
Last seen 28 minutes ago
Wageningen University, Wageningen, the …

"The first column, baseMean, is a just the average of the normalized count values, dividing by size factors, taken over all samples."

See e.g. Mike's workflow published at the F1000 here (section "Building the results table").

 

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Thanks! If a lot of differential taxa between compared groups were found by Deseq based on the microbiota data, is it necessary to set a cutoff for Basemean to keep more "prevalent" taxa as setting cutoffs for p value and FDR? If necessary, what is generally acceptable cuoff for Basemean?

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You can choose your own cutoff, and I have no input on what would be an appropriate level for mibrobiota.

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kledo577 • 0
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Last seen 10 weeks ago
Vietnam

Its meaning lies here (Drift Hunters)

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