Paired-test between two groups within a condition after phyloseq_to_deseq2
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trichorico • 10
Last seen 3 days ago

I have 3 sample groups "Group": White_lion (n=25), Black_lion (n=5), White_tiger (n=28) with taxa groups.

When I run the phyloseq to DEseq2 using

diagdds = phyloseq_to_deseq2(physeq, group="letters")
gm_mean = function(x, na.rm=TRUE){
  exp(sum(log(x[x > 0]), na.rm=na.rm) / length(x))
geoMeans = apply(counts(diagdds), 1, gm_mean)
diagdds = estimateSizeFactors(diagdds, geoMeans = geoMeans)
diagdds = DESeq(diagdds, fitType="local")

res = results(diagdds)
res = res[order(res$padj, na.last=NA), ]
alpha = 0.01

sum(res$padj < alpha, na.rm=TRUE)

sigtab = res[(res$padj < alpha), ]
# Add taxonomic labels for plotting
sigtab = cbind(as(sigtab, "data.frame"), as(tax_table(physeq2)[rownames(sigtab), ], "matrix"))


I obtain 17 differentially abundant taxons (I assume this takes the first group alphabetically, and compares to the other two independently of their group size? -- is this correct?)

But I am really interested in to compare A to B, and A to C. (White lion to black lion; and white lion to white tiger). How can I include two-group test within my group comparison?

  • Should I run separately these by creating a new phyloseq only containing these features?
  • Could I maybe run something like this
    diagdds = phyloseq_to_deseq2(physeq2, ~ Animal + Colour)
    I end up with 23 significant features,

How can I obtain differentially abundant features between paired-groups?


DESeq2 phyloseq • 111 views
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Last seen 1 day ago
United States

You don't have to assume how the functions work, just read the documentation. The vignette discusses how results works, as does ?results. In particular see the contrast argument.

In addition, I'm skeptical of the use of DESeq2 testing for microbiome/metagenomics. So I won't comment on whether more or less DA features is indicating anything meaningful.

Entering edit mode

Thanks Michael, I'll keep playing around with the contrast function. When I said "I assume" I mean "this is why I understood from the vignette", which is already pretty explanatory.

Is there a way of keeping track of the changes of the vignette every time you upgrade a new version? Thank

Entering edit mode

Honestly there isn't too much change in the past versions.

As far as functions, any meaningful change goes in the NEWS file.

If you want to monitor changes to vignette you could look here:


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