Paired-test between two groups within a condition after phyloseq_to_deseq2
0
Entering edit mode
trichorico • 10
@9b83e781
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"))

dim(sigtab)

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?

Thanks

DESeq2 phyloseq • 111 views
ADD COMMENTlink
2
Entering edit mode
@mikelove
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.

ADD COMMENTlink
1
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

ADD REPLYlink
1
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:

https://github.com/mikelove/DESeq2/blame/master/vignettes/DESeq2.Rmd

ADD REPLYlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 224 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.4