An end to end workflow for differential gene expression using Affymetrix microarrays

Abstract

In this article, we walk through an end–to–end Affymetrix microarray differential expression workflow using Bioconductor packages. This workflow is directly applicable to current “Gene” type arrays, e.g. the HuGene or MoGene arrays but can easily adapted to similar platforms. The data re–analyzed is a typical clinical microarray data set that compares inflammed and non–inflammed colon tissue in two disease subtypes. We will start from the raw data CEL files, show how to import them into a Bioconductor ExpressionSet, perform quality control and normalization and finally differential gene expression (DE) analysis, followed by some enrichment analysis. As experimental designs can be complex, a self contained introduction to linear models is also part of the workflow.