--- title: "H. Integrative Analysis" author: Martin Morgan (mtmorgan@fredhutch.org) date: "`r Sys.Date()`" output: BiocStyle::html_document: toc: true vignette: > %\VignetteIndexEntry{H. Integrative Analysis} %\VignetteEngine{knitr::rmarkdown} \usepackage[utf8]{inputenc} --- ```{r style, echo=FALSE, results='asis'} BiocStyle::markdown() ``` # Scope and opportunity ## Case study 1: TCGA Copy Number / Expression # Accessing 'Consortium' data # Representing integrated data sets ## Key components Samples - Including 'phenotypic' attributes measured on each Assays - Often, rectangular features x samples `matrix()` of values - A different representation: `data.frame()` of feature, sample, value tuples. Experiments - Sample inputs to each experiment - Assay outputs from each experiment - Additional experiment-specific information, each date on which samples were processed ## Alternative Representations R-based representations Other approaches - Data base - 'Scientific' representations, e.g., [HDF5](http://www.hdfgroup.org/HDF5/) - 'Computational' representations, e.g., [HDFS](http://hadoop.apache.org/docs/r1.2.1/hdfs_design.html) ## A preliminary design # Statistical and other challenges # Practical