/odp_general_studies

Reproducible analyses for "The optimal discovery procedure for significance analysis of general gene expression studies" by Bass and Storey

Primary LanguageTeX

This contains the code used in the pre-print.

Overview of directories:

  • simulations/:

    • 00-analyze-experiments.R: analysis of the experiments in the paper.
    • 01-combine_objects.R: merges the datasets from 00-analyze-experiments.R.
    • 02-main_simulations.R: contains the steps code used to generate the simulated data in Figure 5. Note that 02-run_simulations.R is code used to execute the code on the cluster.
    • 03-summarize_simulations.R: summarizes the simulation results.

  • data/:

    • Data output from simulations/. See subdirectory for descriptions.

  • analysis/:

    • main_figures.Rmd: R markdown file to reproduce the figures in the manuscript.
    • kidney_filter_probes.R: code used to filter kidney probes.
    • figures/: figure used in manuscript (generated from main_figures.Rmd).

  • manuscript/: contains manuscript.