I am new to bioinformatics, I want to code GSEA using gene profiles derived from the GEO database and using my custom gene set. How do I calculate the Enrichment score for each of the cohort in the GEO data set and get the p-values for distributions generated from k random permutations
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stewiegriffin •
Thanks for the link, GSEA could not rank the gene with only a single cohort.
How could I create a rank list with a data set having multiple profiles, but no control to compare with.
You must need one metric to rank the data. Because, the algorithm looks if there are enriched set at the top or bottom of a ranked list. Then you can run gseapreranked. How are your profiles created? Isn't there any metric which can rank the genes in the profile?
I am using the profiles from this data set( https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22886) [HGU133A]. The expression levels of various probes are listed but can I use it to create a rank list.
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Read the FAQ: http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/FAQ
The various scenario of running GSEA are clearly explained there.