Re: [gsea-help] ssGSEA output
Anthony Castanza
Hello,
Yes, the output of ssGSEA is a sample by gene set table of enrichment scores. These scores are calculated by internally ranking the expression values for each sample by the z-score so the positive scoring gene sets contain genes which are disproportionately represented at the top of the list, and the negatively scoring gene sets genes are disproportionately at the bottom of the list.
Let me know if you have more questions about this method.
-Anthony
Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego
From:
gsea...@googlegroups.com <gsea...@googlegroups.com> on behalf of Anglin Dent <angli...@gmail.com>
Date: Wednesday, May 19, 2021 at 1:31 PM
To: gsea-help <gsea...@googlegroups.com>
Subject: [gsea-help] ssGSEA output
Hi there,
can someone tell me if the ssGSEA output is the enrichment score? Seems unclear since the values are in the hundreds. Also, would someone be able to clarify what a negative value in this output file would indicate?
Thanks!
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Anthony Castanza
ssGSEA calculates relative enrichments of a collection of gene sets within a single sequenced sample (designed to be used on within-sample normalized expression data, like TPM), Classical GSEA is designed to be used to calculate differential enrichment between two groups of sequenced samples, (or correlated along a continuous vector such as a time course) using counts normalized for between-sample comparisons.
It’s entirely conceivable that the relative positions of genes in a gene set could change between samples, but the absolute expression levels of the genes in the set are relatively constant. So which method you use is dependent on the information you want – relative or absolute change. Generally, most people want the classical GSEA approach but it will depend.
Also, how are you calculating significance for the ssGSEA results? ssGSEA by default does not perform significance testing so I can’t really comment there. I’m not sure I fully understand how you’re combining and comparing the ssGSEA and standard GSEA results here.
-Anthony
Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego
From:
gsea...@googlegroups.com <gsea...@googlegroups.com> on behalf of Anglin Dent <angli...@gmail.com>
Date: Thursday, May 27, 2021 at 9:18 AM
To: gsea-help <gsea...@googlegroups.com>
Subject: Re: [gsea-help] ssGSEA output
Hi Anthony,
Thanks for your help! I just had a question about the difference between ssGSEA and GSEA. If I am examining pathway enrichment within different regions within a single sample, do you think ssGSEA would be a more appropriate metric than GSEA? Would it make sense that in my ssGSEA results there are significant differences in pathway enrichment scores across the different regions, but when doing GSEA analysis across my entire cohort of samples differences in pathway enrichment scores within a single sample are not significant? Which analysis would be more appropriate?
Thank you so much!
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