README

################################################################################
# git repository for the paper:                                                #
#                                                                              #
#            Unaccounted uncertainty from qPCR efficiency estimates            #
#                   entails uncontrolled false positive rates                  #
#                                                                              #
#                           Bilgrau et al. (2015)                              #
#                                                                              #
################################################################################

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.