Question: Deseq: What does "BaseMean" mean?
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9 months ago by
1832278510 wrote:
Deseq: What does BaseMean (output of deseq) mean? I cannot find its description in the manual.
deseq2 • 607 views
modified 9 months ago by Guido Hooiveld2.5k • written 9 months ago by 1832278510

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?

Answer: Deseq: What does "BaseMean" mean?
1
9 months ago by
Guido Hooiveld2.5k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.5k wrote:

"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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Also see here:

https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#access-to-all-calculated-values

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?