Scoring scheme in GSEA

Question

[vivien.wee16]

Hi,

What is the difference between classic and the default weighted p=1 under the scoring scheme in GSEA?

Answer 1

[Santosh Anand]

From FAQ

Enrichment statistic. To calculate the enrichment score, GSEA first walks down the ranked list of genes increasing a running-sum statistic when a gene is in the gene set and decreasing it when it is not. The enrichment score is the maximum deviation from zero encountered during that walk. This parameter affects the running-sum statistic used for the analysis. The last section of the Gene Set Enrichment Analysis PNAS paper shows the mathematical descriptions of the methods used in GSEA. This option controls the value of p used in the enrichment score calculation shown there:

▪ classic: p=0

▪ weighted (default): p=1

▪ weighted_p2: p=2

▪ weighted_p1.5: p=1.5

Also see Enrichment Score ES(S) in original paper