MergingHD

This repository contains the code used in the study presented in the paper "Merging Microarray Studies to Identify a Common Gene Expression Signature to Several Structural Heart Diseases" by Olga Fajarda, Sara Duarte-Pereira, Raquel M. Silva and José Luís Oliveira.

Folder Additional Files

This folder contains the additional files of the paper.

Folder data

This folder contains the data obtained after the pre-processing:

• all_before_rem_batch: expressions obtained after the pre-processing;
• all_id: identification of the sequences through the GB accession number;
• all_platform: identification of the platform used to obtain the expressions;
• all_samples: identification of the samples;
• all_type: class of every sample (D: diseased or Z: control).

Folder script

This folder contains the scripts used:

• batchRemoval_ComBat: remove the batch effect;
• featureSelection_limma: feature selection using limma package;
• plot_mds_after: plot MDS using the expression after removing the batch effect;
• plot_mds_before: plot MDS using the expression before removing the batch effect;
• preprocessing: data pre-processing;
• randomForest: Random Forest algorithm;
• select_train_test: divide the dataset into a training set (70% of the samples) and a test set (30% of the samples).