Hi,

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?

Regards,

Nelly

*tutorial: http://joey711.github.io/phyloseq-extensions/DESeq2.html

hi,

Take a look at the DESeq2 vignette:

vignette("DESeq2")

This discusses how to extract multiple results tables after running DESeq(): 

"The contrast argument of the function results takes a character vector of length three: the name of the variable, the name of the factor level for the numerator of the log2 ratio, and the name of the factor level for the denominator..."

and you can also look at help for a specific function. What you want to use is the contrast argument of the results() function:

?results

Many thanks Michael!

Nelly