detect_notDetect for qPCR detection

[miwa582]

Currently we have detect_notDetect to call 0/1 of target taxon in qPCR. However it is unclear if it's for each technical replicate or for biological replicate.

Q1. Do we need 2 terms here to distinguish? i.e., detect_notDetec_techRep, detec_notDetect_bioRep

Q2. If we create these terms, detect_notDetec_techRep should be in ampData (amplification data), but what about detect_notDetect_bioRep? Should this go to sampleMetadata instead of ampData?

[miwa582]

We need both detect_notDetect for both bioRep and techRep. Some people would get the average Ct/Cq or copy number for a biological replicate (bioRep) and call 1/0 from the single averaged value. In this case, there is no need of detect_notDetect_techRep. However, some (including @CeciliaVR ) call 1/0 for each techRep (based on the threshold of estimated copy numbe or Ct/Cq), and then decide 1/0 for the bioRep based on the # of 1s from techReps. In this case, detect_notDetec for both bioRep and techRep would be needed.

I prefer having detect_notDetect_bioRep in ampData right after detect_notDetec_techRep. In this case, 0/1 call for detect_notDetect_bioRep would be repeated across the whole techRep within the sample. But I think having the output related info (e.g., Ct/Cq, extimated copies, and 0/1) in one place.
I know that's now what @chelbing and Nick suggested in the manuscript comments... (They suggested to have it in sampleMetadata)