# GSEA To run a GSEA analysis, click on the 3 dot column menu at the top of a categorical column (not a numerical column) and choose 'GSEA'. This will take you to new page where you will define the sample subgroups you would like to compare (note that you can select multiple categories for a single subgroup). After you have your subgroups, choose a gene set library, scroll to the bottom and click 'submit'. {% hint style="warning" %} Due to compute limitations you can only run a total of 2000 samples through the analysis pipeline. {% endhint %} This will start the analysis, which make take a while to run depending on the size of the dataset. As the results are completed, the web page will update. Scroll to see more results. Once the analysis is finished it will say 'Done' at the top of the page. ## More details The gene expression dataset chosen for a specific study/cohort is the same gene expression dataset as the one in the [Basic Datasets menu](/project/overview-of-features/visual-spreadsheet.md#selecting-a-dataset). The Advanced Visualization parameters apply to the PCA or t-SNE plot, as well as the blitzGSEA analysis itself. Note that the GSEA analysis runs [blitzGSEA](https://academic.oup.com/bioinformatics/article/38/8/2356/6526383), a faster implementation of a traditional GSEA analysis. ## Running it on your own data We disable running our GSEA analysis on your own data since we send the data in the analysis to various websites, which may not be secure. Currently we only offer a [docker image](https://gallery.ecr.aws/f8e3p8q3/xenablitzgsea) as a method for running this pipeline on your own data. Please contact us if you need help setting this up. --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://ucsc-xena.gitbook.io/project/overview-of-features/gsea.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.