Can I apply combat and refBase on EPIC v2 data ? I ask the question because of the following. If I run DMP on normalized data or normalized data corrected with Combat, I get a large number of significant changes. However, if I run DMP on data that has gone through normalize + Combat + RefBase, I don't get any significant changes at any threshold of padjusted.
Can I apply combat and refBase on EPIC v2 data ? I ask the question because of the following. If I run DMP on normalized data or normalized data corrected with Combat, I get a large number of significant changes. However, if I run DMP on data that has gone through normalize + Combat + RefBase, I don't get any significant changes at any threshold of padjusted.
Thank you for your advice.