Off topic:Gene Set Enrichment Analysis parameters
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9.2 years ago
Mo ▴ 920

Hello,

As I mentioned in my previous question How to perform Gene Set Enrichment Analysis

I am trying to perform GSEA, I finally managed to build my data according to the structure of GSEA software from broadinstitute . Now I am trying to set the paramaters which I face a problem and I could not find a solution in the internet. The parameters are as follows:

Expression dataset 
Gene sets database
Number of permutations
phenotype labels
collapse dataset to gene symbols 
permutation tupe
chip platform

I don't know what to choose for the gene sets database. I selected one of those which appears by itself, but I get error. Anyone knows how to fix this ? or how to select the parameters?

gene • 3.0k views
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