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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 • 29k views

ADD COMMENT • link written 6.4 years ago by 183227851 • 0

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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?

ADD REPLY • link 6.4 years ago 183227851 • 0

score 2 · Answer 1 · 2018-09-20

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Guido Hooiveld ★ 4.1k

@guido-hooiveld-2020

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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").

ADD COMMENT • link 6.4 years ago Guido Hooiveld ★ 4.1k

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Also see here:

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

ADD REPLY • link 6.4 years ago Michael Love 43k

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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?

ADD REPLY • link 6.4 years ago 183227851 • 0

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

ADD REPLY • link 6.4 years ago Michael Love 43k