msqrob2guiTutorial.Rmd

---
title: Tutorial on msqrob2 with the GUI
author: "Lieven Clement"
date: "[statOmics](https://statomics.github.io), Ghent University"
output:
    html_document:
      theme: cosmo      
      code_download: false
      toc: false
      toc_float: false
      number_sections: false
bibliography: msqrob2.bib

---

<a rel="license" href="https://creativecommons.org/licenses/by-nc-sa/4.0"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png" /></a>

# Additional resources

- [Install msqrob2 software](./software.html)
- [Download data](https://github.com/statOmics/hupo21/archive/refs/heads/data.zip)

# Heart example

<iframe width="560" height="315"
src="https://www.youtube.com/embed/ZZ89tCCcA7M"
frameborder="0"
style="display: block; margin: auto;"
allow="autoplay; encrypted-media" allowfullscreen></iframe>


![Figure 3. Heart](./figures/heart.png)

Researchers have assessed the proteome in different regions of the heart for 3 patients (identifiers 3, 4, and 8). For each patient they sampled the left atrium (LA), right atrium (RA), left ventricle (LV) and the right ventricle (RV). The data are a small subset of the public dataset  [PXD006675](https://www.ebi.ac.uk/pride/archive/projects/PXD006675) on PRIDE.

Suppose that researchers are mainly interested in comparing the ventricular to the atrial proteome.
Particularly, they would like to compare the expression between

- the left atrium to the left ventricle
- the right atrium to the right ventricle
- the average ventricular vs atrial proteome and 
- if ventricular vs atrial proteome shifts differ between left and right heart region.