How to assign random effect factor in DESeq2 desing?
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zardbid • 0
@user-24811
Last seen 2 days ago

I am trying to do differential abundance in DESeq2 on my 16s rRNA amplicons. The design of my experiment is Y ~ treatment (as fixed effect factor) + body_site (as fixed effect factor) + treatment*body_site + block (random effect factor). I can't see any argument on the vintage for assigning a random effect factor in my model.

Is it even possible to do linear mixed effect model in DESeq2?

Moreover, I am also interested in seeing the differences in different taxa levels. But, by default the results gives me all the 7 taxa levels. How can I revoke the results of only for phylum or family taxa? Not for their sub-taxa (e.g. down to species).

Much appreciated in advanced.

StatisticalMethod DESeq2 phyloseq • 77 views
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@mikelove
Last seen 2 days ago
United States

We don't have random effects models in DESeq2 (you can scan previous posts for more discussion).

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Thanks Michael Love

I would be appreciated if you could give me a hint on how to use deseq2 for different taxa levels. By default, it gives the results of all taxa at once. While I am interested in knowing the changes at e.g. Order or Family.

Kinds, Farhad

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I don't actually think DESeq2 is a good fit for microbiome data, and don't have any particular recommendations for using it in this context.

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