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How is everyone pulling out features that are higher in abundance in one group versus another, or present in one group versus another? I’ve used estimated marginal means and fold change contrasts (using emmeans and limma R packages) to do this before, but wondering what stats tests others are using to do this.
*Disclaimer, not a statistician*
Volcano plots? This plots the fold change versus p-value (significance). Anything outside some set criteria in both axes would be the ones to look at.
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