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Question: Deseq: What does "BaseMean" mean?
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gravatar for 183227851
11 weeks ago by
1832278510
1832278510 wrote:
Deseq: What does BaseMean (output of deseq) mean? I cannot find its description in the manual.
ADD COMMENTlink modified 11 weeks ago by Guido Hooiveld2.3k • written 11 weeks 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?

ADD REPLYlink written 11 weeks ago by 1832278510
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gravatar for Guido Hooiveld
11 weeks ago by
Guido Hooiveld2.3k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.3k 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").

 

ADD COMMENTlink written 11 weeks ago by Guido Hooiveld2.3k
1

Also see here:

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

ADD REPLYlink written 11 weeks ago by Michael Love20k

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 REPLYlink written 11 weeks ago by 1832278510

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

ADD REPLYlink written 11 weeks ago by Michael Love20k
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