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adityabandla
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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?
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?
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.