Matlab scripts for the manuscript "Statistical validation of multivariate treatment effects in longitudinal study designs" by Madssen et al.
Reproduce Results:
1 - Figure 2 can be reproduced with routine 1 (computations are lengthy and were performed in a computing server) and visualizations with routine 2.
2 - Figures 3 and 4, and Supplementary Figure 1, can be reproduced with routines 3 and 4 (computations are lengthy and were performed in a computing server) and visualizations with routine 2.
3 - Figure 5 can be reproduced with routine 5.
Code Files:
1 - compute_powercurves.m: Simulation script to generate power curves (using routines 10 and 11).
2 - plot_powercurves.m: Script to plot the figures (using routine 12)
3 - pvalues_mvdata_real.m: Generates figures of the p-values in terms of the number of components from simulated data with effects in the measured data (calling routine 8) and the output is stored in D1. Calls routine 6 to fit LiMM_PCA models.
4 - pvalues_mvdata_emb.m: Generates figures of the p-values in terms of the number of components from simulated data with effects embedded in a specific component (calling routine 9) and the output is stored in D2. Calls routine 6 to fit LiMM_PCA models.
5 - NeoAva.m: calls routines 6 and 7 and generates the figure on NeoAva data
- Warning: It assumes access to a folder outside the repo, and actually duplicates the addition of the path in the previous routine
6 - RM_LiMM_PCA_sim.m: Function for doing repeated measures-LiMM_PCA.
7 - import_neoava_geneex.m: Imports NeoAva gene expression data.
- Warning: It assumes access to a folder outside the repo
8 - simulate_mvdata_real.m: Simulates effects in the measured data
9 - simulate_mvdata_emb.m: Simulates effects embedded in a specific component
10 - powercurves_real.m: Generates power curves from simulated data with effects in the measured data (calling routine 8). Calls routine 6 to fit LiMM_PCA models.
11 - powercurves_emb.m: Generates power curves from simulated data with effects embedded in a specific component (calling routine 9). Calls routine 6 to fit LiMM_PCA models.
12 - collect_results.m: Reads data from simulated results
13 - preprocess2D.m: auxiliary fuction taken from the MEDA Toolbox v1.3
14 - create_design.m: auxiliary fuction taken from the MEDA Toolbox v1.3
Data:
D1 - sim_real.mat: data simulated with effects in the measured data
D2 - sim_emb.mat: data simulated with effects embedded in a specific component
Folders:
F1 - Figures: figures obtained from simulations
F2 - Script_Real: data generated for power curves VarReal
F3 - Script_Emb: data generated for power curves VarHigh5
F4 - html: web page with the figures obtained from simulations