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This data set was collected to provide examples and aid in developing a standardized way of determining LOD and LOQ for eDNA assays and has 3 data files. GEDWG_LOD_DATA3.csv is raw qPCR data from multiple labs running multiple standards of known concentration for eDNA assays they regularly use. Comparison-Data.csv is the merged data output from running a generic LOD/LOQ calculator script multiple times with different LOD model settings. The generic LOD/LOQ calculator script is available at: https://github.com/cmerkes/qPCR_LOD_Calc, and details about the multiple settings used are commented in the analysis script available at: https://github.com/cmerkes/LOD_Analysis
Categories: Data;
Tags: Environmental DNA,
PCR,
USGS Science Data Catalog (SDC),
Whitney Genetics Laboratory, 555 Lester Avenue, Onalaska, Wisconsin, 54650,
biota, All tags...
detection,
eDNA,
invasive species, Fewer tags
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This script is designed to analyze qPCR data for many replicates of known concentration DNA standards and determine the limit of detection (LoD) and limit of quantification (LoQ) for use in environmental DNA applications. It is written in the hopes that users with even limited knowledge of R will be able to successfully use the code to analyze their own data in the same way as other eDNA researchers to get similar results and automatically generate plots to visualize the data. The code has 5 lines for user input and requires a few simple restrictions on the input data, but after that the user should be able to run the code without any further coding or interventions. No R programming ability is required to run this...
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Bighead Carp, Silver Carp and Grass Carp (collectively Asian carp) were introduced to North America in the 1960s and 70s and have established in the lower Mississippi River basin. Previously published evidence for spawning of these species has been limited in the upper Mississippi River to just below Dam 22 (near Saverton, MO). In 2013 and 2014, we sampled ichthyoplankton at 18 locations in the main stem of the upper Mississippi River from Dam 9 through Dam 19 and in four tributary rivers that empty into the Mississippi River (Des Moines, Skunk, Iowa and Wisconsin Rivers). We identified eggs and larvae using morphological techniques and then used genetic tools to confirm species identity. The spawning events we...
Categories: Data;
Types: Citation;
Tags: Asian carp,
Minnesota,
Mississippi River,
USGS Science Data Catalog (SDC),
Upper Mississippi River, All tags...
Wisconsin,
biological invasion,
fish eggs,
invasive species,
larval fish, Fewer tags
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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.
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