I have done GSEA pre-ranked on differentially expressed genes between tumors and normals. The genes have been ordered by log fold change since GSEA pre-ranked requires an ordered list of genes.
The results are outputted in the format with phenotypes as
na_neg. I am not sure about these phenotypes as how does it differentiate between the 2 phenotypes based on an ordered list of genes.
I understand that the normal GSEA when run on tumors and normals expression values gives us the output between these two phenotypes, but not sure what does the phenotype mean in GSEA pre-ranked.
The fold change values are both positive and negative which are an input along with the gene symbols to GSEA pre-ranked in my case.