josecamachop/vasca

Code repository for the paper Variable-Selection ANOVA Simultaneous Component Analysis

Variable-Selection ASCA (VASCA)

This repository contains the code for reproducing the simulation results of the paper Camacho J, Vitale R, Morales-Jimenez D and Gómez-Llorente C. Variable-Selection ANOVA Simultaneous Component Analysis. Submitted to Bioinformatics. 2022

This repository requires the MEDA toolbox v1.3 at https://github.com/josecamachop/MEDA-Toolbox/tree/v1.3

Contact person: José Camacho ([email protected])

Last modification of this document: 3/Nov/22

Organization

The code is organized in a number of Matlab scripts:

• The scripts named "RunExample#" perform the complete computation of the corresponding simulated example in the paper.
• The script named "RunWheat" performs the motivating example with ASCA.

The present repository is organized as follows:

• README.md This document.

• RunExample1.m Contains the code for the example with non-significant relationships.

• RunExample1b.m Contains the code for the example with non-significant relationships in two factors with several levels.

• RunExample2.m Contains the code for the example with significant one-to-one relationships.

• RunExample2b.m Contains the code for the example with significant one-to-one relationships and a small bias.

• RunExample3.m Contains the code for the example with a multivariate relationship.

• RunExample4.m Contains the code for the example with a multivariate relationship in two factors with several levels.

• RunWheat.m Contains the code for the ASCA motivating example.

• html/ Contains the web reports obtained with command "publish".

• Fig/ Contains the figures of the paper.

• example1.mat Contains the workspace after the computation of Example 1 for simuleMV as the simulation engine.

• example1_randn.mat Contains the workspace after the computation of Example 1 for randn as the simulation engine.

• example1b.mat Contains the workspace after the computation of Example 1b.

• example2.mat Contains the workspace after the computation of Example 2.

• example2b.mat Contains the workspace after the computation of Example 2b.

• example3.mat Contains the workspace after the computation of Example 3.

• example4.mat Contains the workspace after the computation of Example 4.

• example5.mat Contains the workspace after the computation of Example 5.

• wheat Contains the wheat data.

• parglm_genes Contains our interpretation of the code of ASCA-genes.