Introduction | Context | Methods | Formats | Managing data and metadata: the SummarizedExperiment and MultiAssayExperiment formats | Importing from/exporting to tabular files | Text and graphical outputs | Hands-on | The sacurine cohort study | reading: reading the data | inspecting: looking at the data | Post-processing | correcting: Correcting signal drift and batch effect | Variable filtering | Normalization | transforming: transforming the data intensities | Sample filtering | hypotesting: univariate hypothesis testing | Unsupervised analysis | Principal component analysis: PCA | clustering: hierarchical clustering | Supervised modeling | Partial Least Squares modeling: (O)PLS(-DA) | Feature selection | annotating: MS annotation | writing: Exporting the results | Graphical User Interface | Working with multi-omics datasets | Appendix | Additional examples of application to single and multiple omics data sets | NCI60_4arrays data set | Cheat sheets for Bioconductor (multi)omics containers | SummarizedExperiment | MultiAssayExperiment | Restoring the annotating method in the phenomis package | Session info | References

Introduction | The biosigner package | Hands-on | Loading | Molecular signatures | Predictions | Working on SummarizedExperiment objects | ExpressionSet format | Working on MultiAssayExperiment objects | MultiDataSet objects | Extraction of biomarker signatures from other omics datasets | Physiological variations of the human urine metabolome (metabolomics) | Apples spikes with known compounds (metabolomics) | Bone marrow from acute leukemia patients (transcriptomics) | Session info | References

The ropls package | Context | Orthogonal Partial Least-Squares | OPLS software | The sacurine metabolomics dataset | Study objective | Pre-processing and annotation | Covariates | Hands-on | Loading | Principal Component Analysis (PCA) | Partial least-squares: PLS and PLS-DA | Orthogonal partial least squares: OPLS and OPLS-DA | Working on SummarizedExperiment objects | ExpressionSet format | Working on MultiAssayExperiment objects | MultiDataSet objects | Importing/exporting data | Graphical User Interface | Comments | Overfitting | VIP from OPLS models | (Orthogonal) Partial Least Squares Discriminant Analysis: (O)PLS-DA | Two classes | Multiclass | Appendix | Additional datasets | Cheat sheets for Bioconductor (multi)omics containers | SummarizedExperiment | MultiAssayExperiment | ExpressionSet | MultiDataSet | Session info | References