Question: is it ok to make changes to a DESEq2 object?
0
gravatar for tospo
5.7 years ago by
tospo50
United Kingdom
tospo50 wrote:

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!

 

rna-seq deseq2 • 1.8k views
ADD COMMENTlink modified 5.7 years ago by Devon Ryan97k • written 5.7 years ago by tospo50
1
gravatar for Devon Ryan
5.7 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

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

ADD COMMENTlink written 5.7 years ago by Devon Ryan97k

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

ADD REPLYlink written 5.7 years ago by tospo50
1

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

ADD REPLYlink written 5.7 years ago by Devon Ryan97k
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