MethodologyMicro

This repository contains the code used in the use cases presented in the paper "Methodology to identify gene expression signature by merging microarray datasets" 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.

Subfolder HF

This subfolder contains the data of the usecase heart failure (HF):

• hf_before_rem_batch: expressions obtained after the pre-processing;
• hf_id: identification of the sequences through the GB accession number;
• hf_platform: identification of the platform used to obtain the expressions;
• hf_samples: identification of the samples;
• hf_type: class of every sample (D: diseased or Z: control).

Subfolder ASD

This subfolder contains the data of the usecase autism spectrum disorder (ASD):

• asd_before_rem_batch: expressions obtained after the pre-processing;
• asd_id: identification of the sequences through the GB accession number;
• asd_platform: identification of the platform used to obtain the expressions;
• asd_samples: identification of the samples;
• asd_type: class of every sample (D: diseased or Z: control).

Folder scripts

This folder contains the scripts used:

• batchRemoval_ComBat: remove the batch effect using ComBat;
• batchRemoval_fsva: remove the batch effect using fsva;
• featureSelection_limma: feature selection using limma package;
• linearSvm: Linear SVM algorithm;
• neuralNetwork: Neural Network algorithm.
• plot_mds: plot MDS using the expression;
• preprocessing_affymetrix: Affymetrix data pre-processing;
• preprocessing_illumina: Illumina data pre-processing
• randomForest: Random Forest algorithm;
• select_train_test: select training and test sets