🧬 Microglia EVs study

This repository contains R scripts and sample data used for metabolomics and extracellular vesicles (EVs) analysis in primary microglia cell related Alzheimer's Disease (AD) research. The pipeline includes data preprocessing, statistical analysis, multiple linear regression, and mediation analysis.

📖 Overview

This project implements:

• Data Import & Preprocessing: Reads Excel-based omics datasets.
• Statistical Testing: T-tests, ANOVA, normality, and variance tests.
• Metabolomics Analysis: Outlier detection, Cliff’s Delta calculation.
• Multiple Linear Regression (MLR): Identifies relationships between variables.
• Mediation Analysis: Explores potential mediators in metabolic pathways.

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🚀 How to Run

To execute the full analysis pipeline, run:

source("main.R")

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📊 Pipeline Details

1️⃣ Data Import & Preprocessing

📂 Scripts Used:

src/import_data.R src/metabolite_outliers.R

Description:

• Loads metabolomics and EV data from .xlsx files.
• Identifies and removes outliers using robust standardization.

2️⃣ Statistical Analysis

📂 Scripts Used:

src/t_test.R src/anova.R src/metabolite_Normality_and_Equal_Variance_test.R

Description:

• T-tests and ANOVA to compare groups.
• Shapiro-Wilk test for normality.
• Levene’s & Bartlett’s tests for homogeneity of variance.

3️⃣ Cliff’s Delta Calculation

📂 Script Used:

src/cliff_delta.R

Description:

• Calculates Cliff’s Delta, a non-parametric effect size measure

4️⃣ Multiple Linear Regression (MLR)

📂 Script Used:

src/multiple_linear_regression_mediation_analysis.R

Description:

• Performs multiple linear regression (MLR) across datasets:

1. Group vs Cell
2. Cell vs Media
3. Group vs Media
4. Cell vs EV
5. Group vs EV

• Adjusts p-values using Benjamini-Hochberg correction.

5️⃣ Mediation Analysis

📂 Script Used:

src/multiple_linear_regression_mediation_analysis.R

Description:

• Identifies metabolic mediators between variables.
• Integrates MLR results with mediation models.

6️⃣ Publication

Seong-Hun Bong, Hayoung Choi, Hyun-Ho Song, Dong Kyu Kim, Inhee Mook-Jung, Do Yup Lee (2025).
Metabolic Reprogramming in Primary Microglial Cell and Extracellular Vesicle Triggered by Aβ Exposure.
https://doi.org/10.1111/jnc.70030