Often samples are rerun in later batches to help with differences in kits used to process the samples. The Biomarker Core has generally recommended using the earlier processed sample (earlier batch). I recommend reviewing the methods documents associated with the specific datasets you are working with (if you haven’t already) to see if they provide any recommendations for deciding which one to use. Those documents also typically include a contact for questions, as the folks who generated the data are generally in the best position to provide guidance.
Danielle
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