https://github.com/aebilgrau/effadj

Variance approximations of efficiency adjusted delta-delta-Cq-values
https://github.com/aebilgrau/effadj

Last synced: 8 days ago
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Variance approximations of efficiency adjusted delta-delta-Cq-values

• Host: GitHub
• URL: https://github.com/aebilgrau/effadj
• Owner: AEBilgrau
• Created: 2015-06-08T08:29:25.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2016-04-04T20:45:24.000Z (over 8 years ago)
• Last Synced: 2024-10-31T03:28:18.282Z (8 days ago)
• Language: R
• Homepage:
• Size: 626 KB
• Stars: 2
• Watchers: 4
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README

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README

        
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# git repository for the paper:                                                #

#                                                                              #

#            Unaccounted uncertainty from qPCR efficiency estimates            #

#                   entails uncontrolled false positive rates                  #

#                                                                              #

#                           Bilgrau et al. (2015)                              #

#                                                                              #

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This is the git repository for the paper on estimation of amplification

efficiency in qPCR experiments and the effects of disregarding the uncertainty

hereof. The paper illustrates how to obtain variance approximations of the

efficiency adjusted delta-delta-Cq-values and better account for all sources of

variation in qPCR experiments.

# How to compile and generate the paper

The paper is written in using the R-package knitr (`.Rnw`) document. Please make

sure that R and LaTeX is installed. Likewise, make sure that the needed

R-packages (seen in scripts/master.R) are installed.

The results of the paper and the pdf document can be generated in multiple ways:

(1) If you use Rstudio, open `paper-qPCR.Rproj` and press compile document.

(2) From within `R` run:

    install.packages("knitr")

    knitr::knit('effadj.Rnw')

and afterwards compile the generated `.tex` file using `pdflatex` either via

your favorite TeX editor or the command line.

(3) From the terminal run:

    cd path/to/effadj/knitr

    Rscript -e "knitr::knit('effadj.Rnw')"

    pdflatex effadj.tex

Please cite our paper if you use code, methodology, or results from the paper.