I try to apply GSEA on my data. However, I am a bit confused about the process. For example, I have 10000 genes in my gene expression data. As I understood, firstly I should converted the gene names into appropriate gene ID, like gene symbols. Then, I will download gene sets from database, like Msigdb. The last step is to write function of GSEA and run it. However, Which gene sets should I download ? According to what ? Last but not least, do those gene sets present us to signature of up- and down- regulation ?
Thank you very much in advance !