Single sample GSEA analysis

Question

[tujuchuanli]

Hi,

I sorted specific type of cells by FACS and subjected it to RNA-seq. I want to test the enrichment of target cell type. I want to perform analysis just like GSEA to show the enrichment and get the plot which is common for GSEA (bellowing is an example for the plot which I want). However, I have just one RNA-seq data. I tested ssGSEA and GSVA which can only return a score. My question is can I get the enrichment plot by single sample data?

Answer 1

[jv]

If you only have one sample, you can run GSEA with a user created preranked list of genes as described in the user guide at http://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideTEXT.htm#_Metrics_for_Ranking

If your dataset contains only one sample, GSEA cannot rank the genes; however, you can rank the genes and then use the GSEAPreranked Page to analyze your ranked list of genes.

For more details, see http://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideTEXT.htm#_GSEAPreranked_Page

[tujuchuanli]

Hi jv,

Thank you for your help. But I am still uncertain. The GSEA tools can process the preranked list. However, it still required that I rank the list by a certain criterion before GSEA calculation. Since I have only one sample, is it reasonable that I rank the gene list by the absolute expression value like FPKM and then subject it to GSEA tool?

[jv]

Since I have only one sample, is it reasonable that I rank the gene list by the absolute expression value like FPKM and then subject it to GSEA tool?

yes