Hi, I'm a beginner of R and Python, and also beginner of Bioinformatics. (I'm graduated school's student and I just start that few months ago) I'm finding best package for what I want to do.

I want to do GSEA and make GSEA plot by enrichplot package. (https://yulab-smu.top/biomedical-knowledge-mining-book/enrichplot.html)

My data has 'Affy probe ID', 'adj.P.Value', 'P.Value', 'log2FC', 'Gene.symbol' and 'Gene.title'... How can I do GSEA with Chip(Affy_U133) by my data?

If is it possible, I want to make same plots with GSEA software(Msigdb) May anyone recommend the packages for me?

And, if you know any good guide texts for beginner, I hope you send it to me!

Thank you for your help.

Choi

The book you link to is 'a good guide text for beginners'. Have you read it?