is it ok to make changes to a DESEq2 object?

Question

[tospo]

In DESEq2 is it ok to remove samples or genes from a DESeqDataSet object or do I need to re-build the object every time I want to do that? What if I have already calculated results, do I then need to re-run them?

Thanks for your help!

Answer 1

[Devon Ryan]

You can subset a DESeqDataSet without issues. If you've calculated results from it, then you'll need to recalculate them.

[tospo]

so basically just repeat the dds<-DESEq2(dds) right? I guess it is also ok to change the design formula in this way, right?

[Devon Ryan]

Yeah, you can make any changes you want and then rerun things like that.