Code to analyze multi-lab LOD / LOQ study data

Citation

Merkes, C., Klymus, K., Allison, M., Goldberg, C., Helbin, C., Hunter, M., Jackson, C., Lance, R., Mangan, A., Monroe, E., Piagio, A., Stokdyk, J., Wilson, C., and Richter, C., 2019, Reporting the limits of detection (LOD) and quantification (LOQ) for environmental DNA assays: Data: U.S. Geological Survey data release, https://doi.org/10.5066/P9AKHU1R.

Summary

This code supports the manuscript "Reporting the limits of detection (LOD) and quantification (LOQ) for environmental DNA assays". The code analyzes outputs generated by another more generic code to analyze raw qPCR data for LOD and LOQ. This code requires the generic LOD / LOQ calculator script to read in and prepare the data, with additional script runs as described in comments within this code. We wrote this code to specifically analyze our data and generate the figures for the above-mentioned manuscript, however it could be adaptped by a savvy programmer to run similar analyses.

Summary

This code supports the manuscript "Reporting the limits of detection (LOD) and quantification (LOQ) for environmental DNA assays". The code analyzes outputs generated by another more generic code to analyze raw qPCR data for LOD and LOQ. This code requires the generic LOD / LOQ calculator script to read in and prepare the data, with additional script runs as described in comments within this code. We wrote this code to specifically analyze our data and generate the figures for the above-mentioned manuscript, however it could be adaptped by a savvy programmer to run similar analyses.

Contacts

Point of Contact :: Christopher M Merkes
Originator :: Christopher M Merkes, Katy E Klymus, Michael Allison, Caren S Goldberg, Caren Helbin, Margaret E Hunter, Craig A Jackson, Richard Lance, Anna Mangan, Emy Monroe, Antoineete Piagio, Joel P Stokdyk, Chris Wilson, Cathy A Richter
Metadata Contact :: Christopher M Merkes
Distributor :: U.S. Geological Survey - ScienceBase

Attached Files

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LICENSE	307 Bytes	text/plain
LoD-Analysis.R	39.96 KB	text/x-rsrc
README.md	2.7 KB	text/x-web-markdown

Related External Resources

Type: Related Primary Publication

Klymus, K.E., Merkes, C.M., Allison, M.J., Goldberg, C.S., Helbing, C.C., Hunter, M.E., Jackson, C.A., Lance, R.F., Mangan, A.M., Monroe, E.M., Piaggio, A.J., Stokdyk, J.P., Wilson, C.C., and Richter, C.A., 2019, Reporting the limits of detection and quantification for environmental DNA assays: Environmental DNA, v. 2, no. 3, p. 271–282, https://doi.org/10.1002/edn3.29.	https://doi.org/10.1002/edn3.29

Code to analyze multi-lab LOD / LOQ study data

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