I ran DESeq2 on different samples with three varying factors. For analysis I always kept two factors constant and then ran DESeq2 on one factor (always the same) to check for upregulated genes.
So in the end I ended up with 4 results for upregulated genes. I am now wondering if there is a tool to analyse which one of these factors resulted in the upregulation of those genes.
It could be that the combination of those factors led to the upregulation.
Thank you for your help.
If you want to keep using
DESeq2 try two more runs, each using just one of the control factors plus the test factor, then compare.
The alternative is to use a tool that allows for contrast factors (Limma, EdgeR).