ABSTRACT
This chapter shows how to retrieve data from several public repositories and some basic analysis that can be performed on the data. It introduces the functions and packages in R/Bioconductor that can be used to perform specific queries, retrieval, and analysis, all within a single R session. Accessibility to primary data has been strongly motivated by the research community to encourage reproducibility of results. In addition to reproducibility, the access to primary data has motivated the testing of novel methodologies. In this case, several different methodologies can be tested on the same dataset and study their differences and commonalities. Association analyses of transcriptomic data for case/control studies are performed to describe the differences in transcriptomic patterns between the groups of subjects. The cancer genome atlas can be fully accessed and analyzed with R/Bioconductor. A wealth of clinical, genomic, transcriptomic and methylomic data, amongst others, are accessible for novel inferences, integration, replication and validation of previous results.
