Ebook: Bioconductor Case Studies

Preface -- Contents -- List of Contributors -- 1 The ALL Dataset -- 1.1 Introduction -- 1.2 The ALL data -- 1.3 Data subsetting -- 1.4 Nonspecific filtering -- 1.5 BCR/ABL ALL1/AF4 subset -- 2 R and BioconductorIntroduction -- 2.1 Finding help in R -- 2.2 Working with packages -- 2.3 Some basic R -- 2.3.1 Functions -- 2.3.2 The apply family of functions -- 2.3.3 Environments -- 2.4 Structures for genomic data -- 2.4.1 Building an ExpressionSet from .CEL and other files -- 2.4.2 Building an ExpressionSet from scratch -- 2.4.3 ExpressionSet basics -- 2.5 Graphics.;In this volume, the authors present a collection of cases to apply Bioconductor tools in the analysis of microarray gene expression data. Each chapter describes an analysis of real data using hands-on example driven approaches. Short exercises are included.