I was wondering if it is possible to run DESeq ( or for that reason any other tool for differential expression analysis) to identify significant differences between two organisms (for our research human and mouse).
I know that we have two different sets of genes, but what if we can overcome this problem by giving the genes a neutral ID based on a common variable and take only the genes which are present in both data sets.
We have several RNA-Seq data sets with multiple samples (=replica) from different brain layers in mouse and human. We are doing a DE analysis (DESeq2) to find out which genes are significantly changing between the different brain layers. But we are also interested in changes in the same layer but between the two organisms.
How does it looks like from the statistical point of view?