\contentsline {chapter}{\numberline {1}Introduction}{1}{chapter.1}
\contentsline {chapter}{\numberline {2}Preprocessing overview}{7}{chapter.2}
\contentsline {chapter}{\numberline {3}Preprocessing Affymetrix Data}{19}{chapter.3}
\contentsline {chapter}{\numberline {4}Quality Control of Affymetrix GeneChip data}{53}{chapter.4}
\contentsline {chapter}{\numberline {5}Pre-processing for two-color spotted arrays}{67}{chapter.5}
\contentsline {chapter}{\numberline {6}Cell-based assays}{87}{chapter.6}
\contentsline {chapter}{\numberline {7}SELDI-TOF MS Protein Data}{107}{chapter.7}
\contentsline {chapter}{\numberline {8}Overview of Meta-data Resources and Tools in Bioconductor}{129}{chapter.8}
\contentsline {chapter}{\numberline {9}Querying on line resources}{155}{chapter.9}
\contentsline {chapter}{\numberline {10}Binding annotation data to analysis reports}{173}{chapter.10}
\contentsline {chapter}{\numberline {11}Visualizing Data}{187}{chapter.11}
\contentsline {chapter}{\numberline {12}Distance Measures in DNA Microarray Data Analysis.}{213}{chapter.12}
\contentsline {chapter}{\numberline {13}Design and analysis of differential gene expression studies}{235}{chapter.13}
\contentsline {chapter}{\numberline {14}Cluster Analysis of Genomic Data}{257}{chapter.14}
\contentsline {chapter}{\numberline {15}Machine learning concepts and tools for statistical genomics}{279}{chapter.15}
\contentsline {chapter}{\numberline {16}Multiple Testing Procedures and Applications to Genomics}{303}{chapter.16}
\contentsline {chapter}{\numberline {17}Computational Inference}{349}{chapter.17}
\contentsline {chapter}{\numberline {18}Browser-Based Affymetrix Analysis and Annotation}{371}{chapter.18}
\contentsline {chapter}{\numberline {19}Introduction and motivating examples}{389}{chapter.19}
\contentsline {chapter}{\numberline {20}Graphs}{399}{chapter.20}
\contentsline {chapter}{\numberline {21}Bioconductor software for graphs}{411}{chapter.21}
\contentsline {chapter}{\numberline {22}Statistical Models and Methods for Graphs}{435}{chapter.22}
\contentsline {chapter}{\numberline {23}Case Studies using Graphs on Biological Data}{451}{chapter.23}
\contentsline {chapter}{\numberline {24}Limma}{481}{chapter.24}
\contentsline {chapter}{\numberline {25}Case Study on Microarray Classification}{483}{chapter.25}
\contentsline {chapter}{\numberline {26}From Cel files to lists of interesting genes}{485}{chapter.26}
\contentsline {chapter}{\numberline {A}Appendix}{499}{appendix.A}
\contentsline {chapter}{Index}{523}{appendix*.73}
