10 Differential expression analysis
To learn about differential expression analysis we used the data from the SPEAQeasy-example website we made. This involves work mostly by Nicholas J. Eagles, Joshua M. Stolz, and Louise A. Huuki-Myers. In particular, we followed the set of activities described in detail at SPEAQeasy-example/bootcamp_intro. There are several Bioconductor workflows that also explain how to do differential expression analyses. However, we used the data from SPEAQeasy-example because it has specific properties that are common to the processed data we generate at LIBD, given that we’ve processed a lot of RNA-seq data using SPEAQeasy. Having said that, for more in depth explanations, you might want to check the RNAseq123 and the rnaseqGene Bioconductor workflows that explain how to use packages such as limma and DESeq2.