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  • DESeq2 unknown treatment option?

    Hi all,

    I am wondering how I can include 'unknown' treatment/condition of samples in my design. I have two factors, one is method of mRNA preparation (RiboZero or PolyA), the second is 'responder' or 'non-responder' to a drug that has been administered. There is some missing data here, so about 1/4 of samples are classified 'undetermined response'. At first I thought to include a simple 'unknown' condition, but samples are either responsive to treatment or not. Therefore I thought that classifying a third condition in this way would not make sense. Is there a way to include no information for those samples not designated 'responder'/'non-responder'?

    Thanks, Bruce.

  • #2
    The best approach is to simply exclude the unknown responders.

    Comment


    • #3
      I had considered that as the most realistic option, just wondered if there was a way to use unknowns. Thanks for your input.

      Comment

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