Question

is it ok to make changes to a DESEq2 object?

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9.7 years ago

tospo ▴ 50

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!

DESeq2 RNA-Seq • 3.2k views

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by tospo ▴ 50

score 1 · Answer 1 · 2015-03-09

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9.7 years ago

Devon Ryan 104k

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

ADD COMMENT • link 9.7 years ago by Devon Ryan 104k

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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 REPLY • link 9.7 years ago by tospo ▴ 50

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

ADD REPLY • link 9.7 years ago by Devon Ryan 104k