Question: GSEA on preranked list with weighted enrichment statistic (exponent=1) in R
gravatar for cmgraef
7 months ago by
cmgraef10 wrote:

Hey there!

I'm currently working on a functional analysis of RNAseq data. I've used the GSEA tool by the Broad Institute to obtain quick results and now I'm trying to reproduce the results with R for visualization purposes.

The fgsea is amazingly fast but apparently there is no way to calculate a weighted enrichment statistic which is why my results differ from the original analysis with the GSEA tool. Then I've looked at the DOSE tool as this allows for a weighted enrichment statistic. However, here I can't use the MSigDatabase gene set collection. ClusterProfiler doesn't seem to provide a GSEA preranked option.

Did I miss a function of these packages that would allow me for a GSEA on a preranked list with the MSigDatabase gene set collection and at the same time gives me the option to calculate a weighted enrichment statistic? Is there any other way to solve this problem?

Thank you very much for help in advance!!

Cheers, Moritz

rna-seq dose fgsea • 499 views
ADD COMMENTlink modified 7 months ago by alserg260 • written 7 months ago by cmgraef10

Any ideas? Thank you so much!

ADD REPLYlink written 7 months ago by cmgraef10
gravatar for alserg
7 months ago by
alserg260 wrote:

Could you clarify what exactly you can't reproduce? Both DOSE and ClusterProfiler use fgsea as a backend, so if it's possible with DOSE it should work fine for fgsea.

ADD COMMENTlink written 7 months ago by alserg260
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