DESeq2 Interaction Term Interpretation for Microbiome Data
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ehickman • 0
Last seen 2.6 years ago

Hello, I am working on analyzing 16S microbiome sequencing data using DESeq2. I am very new to this type of work, so apologies if this question has a very obvious answer. I have data from three subject groups (E-cig, non-smoker, smoker), and two sexes (male and female). I am interested in the effect of sex on changes in the microbiome in the different subject groups and I have modeled this using the following code:

deseq_data <- phyloseq_to_deseq2(data, ~ Sex + SubjectGroup + Sex:SubjectGroup)

Which returns these possible results:

> resultsNames(deseq_data)
[1] "Intercept"                         "Sex_M_vs_F"                        "SubjectGroup_E.cig_vs_Non.smoker" 
[4] "SubjectGroup_Smoker_vs_Non.smoker" "SexM.SubjectGroupE.cig"            "SexM.SubjectGroupSmoker" 

What I am confused about (and have tried reading the help pages/vignettes) is what exactly the interaction terms are in comparison to. For example, when I graph the results of "SexM.SubjectGroupE.cig," what is the log2FoldChange data in comparison with? Male non-smokers? I understand that using an interaction term tests for microbes that respond differently to exposure across sexes, but I am struggling the most with the meaning of the log2FoldChange. Any help would be greatly appreciated! Thanks!

deseq2 microbiome • 390 views
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swbarnes2 ▴ 970
Last seen 2 hours ago
San Diego

For interactions, even though the column is labeled "logFold2Change", that's not what it is. Edit: It's the log of the ratio of the fold changes.

I found this site helpful

Look down to the header "The different response in genotypes (interaction term)"

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It's the difference of the log fold changes, not the ratio.


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