ESM1_mite.xlsx (291.05 kB)
freqpcr_data_tables
Supplementary tables for the "freqpcr" paper.
Copyright:
Masahiro Osakabe 2017 (Sheet 1)
Masaaki Sudo 2021 (Sheet 2--)
The quantitative PCR analysis was conducted to quantify the mixing ratios of the R (acaricide resistant) and S (susceptible) alleles of the two-spotted spider mite. As this experiment was the proof-of-concept of the RED-ΔΔCq method, the template DNA solutions were prepared as mixture of R and S at known ratios (the data column "FreqTrue"). PCR conditions and sample pre-treatment are described in Sudo and Osakabe (2021 bioRxiv).
Sheet 2
Example of the data frame of the Cq values ready for the knownqpcr_unpaired() function of freqpcr package.
Sheet 3 and 4
Example Cq data frame ready for the knownqpcr() function of the freqpcr package. Sheet 3 is "not recycled" i.e., allowing NAs. Sheet 4 is "recycled" and missing values are filled with the Cq of the (nearly) corresponding experimental conditions. Both are OK for running knownqpcr() function.
Please read the supplementary material 2 of the freqpcr paper, as well as the PDF help of the R package, to learn how to use the knownqpcr() or knownqpcr_unpaired() functions.
Sheet 5 and 6
Summary table for the output data of Experiment 2 (numerical experiment for the confidence interval of the freqpcr package). See Sudo and Osakabe (2021 bioRxiv) for detail.
