Question: How to do GSEA from gene profiles obtained from GEO
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gravatar for stewiegriffin
2.6 years ago by
stewiegriffin0 wrote:

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

go gsea enrichment gene • 1.6k views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 2.6 years ago by stewiegriffin0
1

Read the FAQ: http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/FAQ

The various scenario of running GSEA are clearly explained there.

ADD REPLYlink written 2.6 years ago by Santosh Anand5.0k
0
gravatar for stewiegriffin
2.6 years ago by
stewiegriffin0 wrote:

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.

ADD COMMENTlink written 2.6 years ago by stewiegriffin0

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?

ADD REPLYlink written 2.6 years ago by Santosh Anand5.0k

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.

ADD REPLYlink written 2.6 years ago by stewiegriffin0
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