Steps 1 and 2 show how to do the same procedure starting from the eset object. It only takes two short steps because DESeq2 is set up to work a lot more nicely with Bioconductor objects than edgeR is. In step 8, we load the eset data with the load() function. Then we use the makeSummarizedExperimentFromExpressionSet() function from the SummarizedExperiment Bioconductor package to convert eset into SummarizedExperiment, which can be used directly in the DESeq() function in step 9. This step works exactly as steps 6 and 7.