Am a beginner with Deseq2, so I might be asking something that's answered elsewhere, in which case I kindly ask for your patience.
Am working with 16S microbiome count data, and I generate my dds object from phyloseq.
dds = phyloseq_to_deseq2(mouth, ~ category)
I am interested in performing tests of how OTUs/species in different oral diseases within the mouth differ compared to healthy patients.
mouth = my phyloseq object
category = 5 different disease states including normal.
I have defined "normal" as the reference category as follows:
dds$category <- relevel(dds$category, ref = "normal")
Then run the test
dds = DESeq(dds, fitType="local")
It all works well, but when I access the results following this tutorial*, I only get a comparison of one of the disease states vs the normal and not the rest.
How can I get the other comparisons if they have been performed? Or how can I perform them if they haven't been tested?