Adjusting for Batch Effects with Linear Models

Lucas Schiffer
June 13, 2017

Data Analysis for the Life Sciences

Topics

  • Introduction
  • P-Value Histograms / Volcano Plots
  • Mathematical Formula
  • Applied Example
  • Exercises

Introduction

  • What are batch effects?
  • Why adjust for them?
  • How to find them?
  • A real world example!

P-Value Histograms / Volcano Plots




P-Value Histograms / Volcano Plots




Mathematical Formula





\[ Y_{ij} = \alpha_j + x_i \beta_{j} + \varepsilon_{ij} \]



\[ Y_{ij} = \alpha_j + x_i \beta_{j} + z_i \gamma_j+\varepsilon_{ij} \]

Applied Example

Exercises

The exercises <- http://rpubs.com/schifferl/abelme