MIG workshop: Linear models

Authors: Saritha Kodikara

Tutors: Ilariya Tarasova, Yidi Deng

Audience	Prerequisites	Duration
Biologists	Intro to R	~ 2.5 hours

Description

This repository includes material for our workshop 'Linear models'. This workshop will introduce the fundamental principles of linear models and linear mixed effect models, with hands-on applications for the analysis of gene expression data, using base and limma R packages.

Installation Requirements

Install R first, then RStudio. Download the most recent version of R and RStudio using the links below:

• R (Preferably R version > 4.0)
• RStudio

Install the R packages. Type the R command lines:

# Install tidyverse package using CRAN
install.packages(c("tidyverse", "nlme", "ggpubr", "MuMIn"))

# Install edgeR and limma packages using BiocManager
if (!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}
BiocManager::install(c("edgeR","limma"))

# Test if packages have been installed
library(tidyverse)  # working with data frames, plotting
library(edgeR)      # cpm, etc -- RNA-Seq normalization
library(limma)      # lmFit, etc -- fitting many models
library(nlme)       # lme
library(ggpubr)     # ggqqplot
library(MuMIn)      # AICc

Material

Click here to access the slides.

Click here to access the HTML workshop document.

Data

All data used for the workshop are in data.zip.

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• The materials were inspired from the workshop r-linear-abacbs2018 from Monash Bioinformatics and QCBS R workshops from Quebec Centre for Biodiversity.