Question: Possible to calculate log odds using DESeq2?
gravatar for adityabandla
20 months ago by
adityabandla10 wrote:

I have a metagenomics dataset, which essentially is a counts matrix (genes as rows and samples as columns). One of my objectives was to identify differentially abundant genes across my sample groups, which I did using DESeq2

I am wondering if its also possible to do some qualitative testing, based on the presence-absence of a gene and quantify that using a metric such as the odds ratio?

ADD COMMENTlink modified 20 months ago • written 20 months ago by adityabandla10
gravatar for Michael Love
20 months ago by
Michael Love17k
United States
Michael Love17k wrote:
We provide only what you see in the results table : LFC, its standard error, Wald (or LRT) test statistic, and p-values.
ADD COMMENTlink modified 19 months ago • written 20 months ago by Michael Love17k

Thanks Michael! I'm sorry if my question is naive, I have been trying to wrap my head around this.

Is it possible to calculate the log odds of a gene being enriched/log odds for a given log2foldchange for pairwise comparisons?

ADD REPLYlink modified 20 months ago • written 20 months ago by adityabandla10

Short answer is that we don't have functionality for log odds of DE in DESeq2.

We offer likelihood ratios. The statistic in the results table when you use test="LRT" is 2*log(likelihood alternative model / likelihood null model). (The 2 comes in so that this statistic can be compared to a chi square distribution.) The log likelihood ratio here is not the same as a posterior odds because we don't estimate a prior odds ratio.

ADD REPLYlink written 19 months ago by Michael Love17k
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