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Question: Possible to calculate log odds using DESeq2?
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gravatar for adityabandla
13 months ago by
adityabandla10
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 13 months ago • written 13 months ago by adityabandla10
1
gravatar for Michael Love
13 months ago by
Michael Love15k
United States
Michael Love15k 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 13 months ago • written 13 months ago by Michael Love15k

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 13 months ago • written 13 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 13 months ago by Michael Love15k
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