I am trying to run a time course DESeq2 analysis with 16S amplicon data in a phyloseq object. All treatments in the time course have the same starting point (T0, time zero).

I ran the following:

df = phyloseq_to_deseq2(GRE.all, ~treatment*day)

and received this error:

Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified. One or more variables or interaction terms in the design formula are linear combinations of the others and must be removed. Please read the vignette section 'Model matrix not full rank': vignette('DESeq2')

DESeq2 time-series data of multiple treatments with common time 0 using the "model.matrix" command to create a full design and reduced design then run LRT. However, I cannot determine how to achieve that with a phyloseq object. So if anyone has any suggestions for how to run a multifactor design on a time series with a common time zero from a phyloseq object, then I am happy to hear them.

Cheers, -Ashley

You could use a design of ~1, as long as you substitute the matrices when you run DESeq()