how to calculate the gene's correlation with phenotype in GSEA ?
For example: two kinds of samples: Ctrl and Exper, GSEA will give a ranking list of genes that related the phenotype Exper. At the same time, can GSEA also give a ranking list of genes that related the phenotype Ctrl? But Does any difference bewteen them?
what is the relationship between phenotype C and phenotype A or B in the original paper about GSEA (Gene set enrichment analysis A knowledge based approch for interpreting geneome wide expression profiles)?