5 - Integrative analysis workshop with TCGAbiolinks and ELMER - Analysis GUI

Introduction

In this section, we will perform the same analysis performed using ELMER, but instead of doing it programmatically we will use TCGAbiolinksGUI (Silva et al. 2017).

First we will launch the TCGAbiolinksGUI.

library(TCGAbiolinksGUI)
TCGAbiolinksGUI()

Downloading data

Please download this two objects:

• Gene expression Summarized Experiment
• DNA methylation Summarized Experiment

Analysis

Create MultiAssayExperiment object

To create the MultiAssayExperiment object go to Integrative analysis/ELMER/Create input data.

Select the DNA methylation object previously downloaded.

Select the gene expression object previously downloaded.