Preprocessing data from genomic experiments. - Preprocessing Overview. - Preprocessing High-density Oligonucleotide Arrays. - Quality Assessment of Affymetrix GeneChip Data. - Preprocessing Two-Color Spotted Arrays. - Cell-Based Assays. - SELDI-TOF Mass Spectrometry Protein Data. - Meta-data: biological annotation and visualization. - Meta-data Resources and Tools in Bioconductor. - Querying On-line Resources. - Interactive Outputs. - Visualizing Data. - Statistical analysis for genomic experiments. - Analysis Overview. - Distance Measures in DNA Microarray Data Analysis. - Cluster Analysis of Genomic Data. - Analysis of Differential Gene Expression Studies. - Multiple Testing Procedures: the multtest Package and Applications to Genomics. - Machine Learning Concepts and Tools for Statistical Genomics. - Ensemble Methods of Computational Inference. - Browser-based Affymetrix Analysis and Annotation. - Graphs and networks. - and Motivating Examples. - Graphs. - Bioconductor Software for Graphs. - Case Studies Using Graphs on Biological Data. - Case studies. - limma: Linear Models for Microarray Data. - Classification with Gene Expression Data. - From CEL Files to Annotated Lists of Interesting Genes. Language: English