Error while generating "molecular function" for Gene Set Enrichment Analysis.

[Adlina Affian]

I am reaching out to you regarding an issue I have encountered while conducting gene ontology analysis for molecular function using your platform.

I have been working with a set of 15 datasets for my research, and I have encountered an error during the analysis process. The error message I received is shown in the attachments. I have reviewed the documentation and support resources available, but unfortunately, I have been unable to find a solution.

Given the importance of this analysis for my research project, I am reaching out to seek assistance in resolving this issue. I would greatly appreciate it if you could provide guidance on troubleshooting this specific error or if there are any updates or patches that may address the issue.

[Yuxing Liao]

Hi Adlina,

As the message suggests, all gene sets do not have 3 overlapping genes from your input, which is unusual for gene ontology. Did you use a very small input gene list? For GSEA, it should just be everything you measured in experiments without prefiltering.

Yuxing

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[Adlina Affian]

Hi Yuxing, 

Yes, I am using very small input gene list, which have a total of 15 gene that having p val <0.01. I do have another list of genes that resulting p<0.05 with 51 gene list. In this case, should I input the 51 gene list instead ?

Thank you

[Alex Saltzman]

If you’re pre-filtering your list you should run ORA not GSEA. 

As stated, running GSEA on data you’ve already subsetted is not proper. 

The choice between prefiltering and running ORA vs not filtering and feeding in all the data with rank order is yours - neither approach is incorrect. 

Sent from my iPhone

On Nov 21, 2023, at 2:29 AM, Adlina Affian <adlina...@gmail.com> wrote:

Hi Yuxing, 

To view this discussion on the web visit https://groups.google.com/d/msgid/webgestalt/2f28f8a4-511d-48d1-9c40-794f662c65den%40googlegroups.com.