As in Recipe 1, the data is provided as both a count matrix and an ExpressionSet object and you can see the Appendix at the end of this book for further information on these object types. The data is in this book's code and data repository at https://github.com/PacktPublishing/R_Bioinformatics_Cookbook under datasets/ch1/modencodefly_eset.RData , datasets/ch1/modencodefly_count_table.txt, and datasets/ch1/modencodelfy_phenodata.txt. Again, we'll use readr and magrittr and, from Bioconductor, SummarizedExperiement, and DESeq2.