Hello,

I am using DESeq2 to assess differences in gene expression between two species. I am testing for differences between the species for 6 different tissue types. General setup:

Species A. tissue 1 Species A. tissue 1 Species B. tissue 1 Species B. tissue 1

Species A tissue 2 Species A. tissue 2 Species B. tissue 2 Species B. tissue 2

I am using the design ~species + tissue (as I do not have enough replicates (~2) per condition to use an interaction model). The contrasts available are "species A vs species B", "tissue 1 vs tissue 2", "tissue 3 vs tissue 4" etc

I want to know the differences in gene expression between species A and B in tissue 1. (i.e. "species A tissue 1 vs species B tissue 1") How can I do this? Please note that different tissues were not collected from the same individuals so I cannot nest individuals within groups.

Thank you very much for your help

For getting started with Bioconductor packages, first check the vignettes and workflows.

Additionally, check the function man pages, e.g. here you are interested in results() so you can type:

?results