Question: Scoring scheme in GSEA
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gravatar for vivien.wee16
11 days ago by
vivien.wee160 wrote:

Hi,

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

gsea • 106 views
ADD COMMENTlink modified 11 days ago by Santosh Anand2.7k • written 11 days ago by vivien.wee160
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gravatar for Santosh Anand
11 days ago by
Santosh Anand2.7k
Santosh Anand2.7k wrote:

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

ADD COMMENTlink written 11 days ago by Santosh Anand2.7k
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