GSEA- RNAseq -three groups

[samy amin]

Hi Anthony

Thanks for your good response to my questions.

I want to find common pathways between three different cancer samples. In the following file, I show you my pipeline and samples. I want to do GSEA  on T4(3 samples ) but I don't know how to use GSEA for three groups.

Thanks.

[Anthony Castanza]

Hi,

 

I'm pretty sure I addressed this in my second reply to your previous thread. There are technical issues with doing this that are best addressed by taking a slightly different approach. My previous reply is copied below:

----
You can't run GSEA on just the commonly regulated genes, but I think there is a way to get to the kind of analysis you want to do.

 

Your S2 comparison is a little complicated due to the two different cancer groups, so the proper way to handle this dataset is definitely though the DESeq2 methods for those kind of confounding variables. This constrains us somewhat in the options for running GSEA, in that you'd probably want all three datasets analyzed the same way if comparing their end results. So if you have the differential expression calculations for T1, T2, and T3 separately, you can use the differential expression calculations from all genes (not just the significant DEGs or common DEGs) in three separate RNK files: 

https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#RNK:_Ranked_list_file_format_.28.2A.rnk.29

One for each comparison. And then you should be able to look for common enrichments by loading the three experiments into Enrichment Map. You would't be able to use the built in GSEA function for this as it doesn't allow multisample comparisons. But on the Cytoscape side there are more elaborate options that let you import multiple datasets. You can find the EnrichmentMap documentation here: https://enrichmentmap.readthedocs.io/en/latest/ I know it has instructions for looking at two samples, and I'm pretty sure it supports more than that.

 

Then using the resulting EnrichmentMap you can find which gene sets are commonly enriched across your samples, and see if the directions are concordant. Might an approach like that work for you?

 ----

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

--
You received this message because you are subscribed to the Google Groups "gsea-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gsea-help+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/b4059b8f-aa5d-414a-b67d-991721845174n%40googlegroups.com.