Recommendation for book: GSEA in R programming

Question

[Amr]

Hello, I am learning how to perform GSEA in R programming, is there an advice for a good recommended book?

Thanks in advance :)

Answer 1

[shiyang_bio]

The standard GSEA software is written in Java. You can use the R package "fgsea" to do similar analysis. Their result should be same, only some little difference in the output figures. Before running "fgsea", you need to rank your genes by some metrics, for example, the fold change or the p-value between two groups(e.g. case vs control). These metrics can be done by DeSeq2, edgeR or limma. Hope this information can help you.