Question: Meaning of zero for ssGESA value calculated by GSVA package
0
gravatar for Shi-Xiang Wang
14 months ago by
China/Shanghai/ShanghaiTech. University
Shi-Xiang Wang0 wrote:

Hello,

After I plot density of ssGSEA method result, I am curious what the zero line means. As the documentation says,

GSVA assesses the relative enrichment of gene sets across samples using a non-parametric approach.

If the mean of distribution locate at left of zero, does it mean this gene list of interest relatively un-enrich comparing with other genes in the genome???

image

Best,
Shixiang

gsva • 326 views
ADD COMMENTlink modified 14 months ago by Robert Castelo2.3k • written 14 months ago by Shi-Xiang Wang0
Answer: Meaning of zero for ssGESA value calculated by GSVA package
1
gravatar for Robert Castelo
14 months ago by
Robert Castelo2.3k
Spain/Barcelona/Universitat Pompeu Fabra
Robert Castelo2.3k wrote:

Hi Shixiang,

We did not develop the ssGSEA method, we just implemented it in the GSVA package. The methodological descriptions in the online manual and the vignette of GSVA refer to the GSVA (deafult) method. The ssGSEA method was introduced by Barbie et al. (2009), where you can find its description in the Online Methods, subsection 'Signature projection method'. That said, GSVA and ssGSEA use both a competitive null hypothesis, meaning that, for each gene set, they compare genes inside the gene set against genes outside the gene set, along a ranking of genes on the basis of their expression. A enrichment score of zero implies that the distribution of the genes inside the gene set along the ranking does not differ from the distribution of genes outside the ranking.

cheers,

robert.

 

ADD COMMENTlink written 14 months ago by Robert Castelo2.3k

Dear Robert,

Thanks for you quick reply. Now I understand what the zero means. So if the mean of enrichment score less much than zero, does it mean that the distribution of the genes inside the gene set  rank significantly low than the distribution of genes outside the ranking? Conversely, if the mean of enrichment score greater much than zero,  the distribution of the genes inside the gene set rank higher?

Best,

Shixiang

ADD REPLYlink written 14 months ago by Shi-Xiang Wang0

Yes. The meaning of GSVA negative scores has been in fact already asked in this support site in this Does GSVA enrichment score comes negative?.

cheers,

robert.

ADD REPLYlink written 14 months ago by Robert Castelo2.3k
Got it, Thank you very much. cheers, Shixiang On 7/19/2018 15:51,Robert Castelo [bioc]<noreply@bioconductor.org> wrote: Activity on a post you are following on support.bioconductor.org User Robert Castelo wrote Comment: Meaning of zero for ssGESA value calculated by GSVA package: Yes. The meaning of GSVA negative scores has been in fact already asked in this support site in this Does GSVA enrichment score comes negative?. cheers, robert. Post tags: gsva You may reply via email or visit C: Meaning of zero for ssGESA value calculated by GSVA package
ADD REPLYlink written 14 months ago by Shi-Xiang Wang0
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