Introduction | Quick start | Creating an EdgeObject | Running differential gene expression with edgeR | Extracting results | Running with limma-voom | Using the convenience function | Session info

Introduction | Installation | Quick start | Loading the package | Working with DesignContrast objects | Building from design and contrast matrices | Visualizing the design | Reading and writing expression data | Read an expression matrix into an ExpressionSet | Read GCT/CLS files | Write ExpressionSet to files | Transforming expression data to long format | Probeset summarization | Filtering probesets | Session info

A simple case study about plate effect: the background | Simulating a study in which randomization is not used | Randomization prevents plate effect from interfering with inferences | Discussions and conclusions

The samples and the conditions | Plate layout requirements | Setting up a BatchContainer object | Moving samples | Running an optimization | Customizing the plate layout | Summary | Session information

Running OSAT optimization | Visualize for plates | Compare scores with various implementations | Run using BatchContainer | Using designit OSAT score implementation | Manually work with data.table | Shuffle optimization with burn-in | Score demonstration

Introduction | Batch effects matter | Go fully random? | designit | Sample Batching | Setup | Optimization | Plate layouts | Continuous confounding | 2-step optimization | Across plate optimization using osat score as before | Within plate optimization using distance based sample scoring function | 2-step optimization multi_plate_layout() | Glimpse on more complex application | Conclusion

Purpose of vignette | Dataset and design task | The animal (sample) sheet | Treatment list | Design constraints and data preparation | Design steps | Assign treatments to animal list | Populate cages | Arrange cages in rack(s)

Sample annotation overview | Task | Optimize batch | Optimization trace | Final batch layout | Repeat but use shuffle with contraints | Optimize runs within batch | Final run layout

Sample annotation overview | Task | Setting up batch container | First optimization with fixed shuffling protocol | Optimization trace | Final batch layout | Perform new iterations on optimized batch container | Optimization with specified stopping criteria | Optimization with multi-variate scoring function | Auto-scaling scores | Passing a customized shuffling function | Using simulated annealing (SA) for optimization | Full blown example

Purpose of the vignette | The design problem | Samples and treatments | Subgroup related constraints | Doing it all in one go | Multiple step approach | Form homogeneous subgroups - pools of animals that could go into one cage | Find all valid ways to allocate treatments to the subgroups | Generate shuffling function for potential study designs | Use shuffling function for optimizing design

Working with Geneset Management System (GeMS) | Background | Examples | Task 1: show genesets provided by a user | Task 2: insert new genesets to GeMS | Task 3: Remove a geneset | Task 4: Retrieve gene-sets with names | Task 5: Retrieve gene-sets with a certain property | Conclusions | Session information

Rescaled Smith functions | Cog sets | Battlement sets

The VDedgeDrawn object | Faces | Joining disjoint faces | The TissueDrawing object | Injecting points and edges | Making a simple drawing from a circle | Circles | Check for the intersection of two edges | Vennerable:::addSetToDrawing two polygons | Vennerable:::addSetToDrawing a polygon and a circle | Invisible edges | Tangents | Three circles | Triangles | Three squares | Noncontigous subsets | Ellipses | Chow Ruskey | This document

Venn objects | The VennDrawing object | Two circles | Two squares | Three circles | Three Triangles | Three Squares | Four squares | Chow-Ruskey | Euler diagrams | Error checking | This document

Overview | Computation and Annotation | Unweighted Venn diagrams | Weighted Venn diagrams | Euler diagrams | Some loose definitions | This document