GSEA preranked with signed -log10 p value

[Luca Sigalotti]

Hi all. I am running a pre-ranked GSEA on a list of genes ranked according to signed -log10 p value. Data are derived from an RNAseq differential expression analysis performed with DESeq2.

The question is, am I correct in selecting weighted as the enrichment statistic?

Thank you for the help.

Best,

Luca

[Anthony Castanza]

Yes, weighted is generally the correct enrichment statistic to use.
Without weighting (for example, in classic mode) GSEA will just use the order of the gene list and the magnitude won't be considered at all.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[Luca Sigalotti]

Thanks,

Luca

[Ramon Garcia Areas]

Hi Anthony, 

Can weighted analyses be done on the GSEA website or can it only be done with the downloaded software?

Best,

Ramón

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[Anthony Castanza]

The GSEA website only performs a simple hypergeometric "overlap statistic" test. The full weighted GSEA test is available through either the desktop application or through a module that can be run online through the (free) GenePattern.org cloud platform.

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

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