Example Dataset from GSEA

[Peter Schumann]

Hello, 

I am trying to use the Leukemia example dataset from the GSEA site: http://www.gsea-msigdb.org/gsea/datasets.jsp

However, when I run a GSEA using the desktop software, it gives me a result that shows enrichment in 1/1 gene sets. Whereas the original data set yields 124 / 182 gene sets as being enriched. 

This dataset is nearly 20 years old -- from 2002. And the original authors used the c1.symbols.gmt gene set database. I am using the most current version of this database. Could it just be that the database has changed that significantly over this time period?

Are there any more up-to-date example datasets I could use instead?

Thank you, 

Peter

[Anthony Castanza]

Hi Peter,

I reran the Leukemia dataset myself and, while I didn't get much in the way of significant hits with C1, you should be seeing more than one gene set in the denominator of that result. What parameters are you using for GSEA? If you're using the dataset in its "_hgu95av2.gct" form you'll need to use the latest "Human_AFFY_HG_U95_MSigDB" chip with Collapse/Remap set to "Collapse".

--
You received this message because you are subscribed to the Google Groups "gsea-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gsea-help+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/35c78395-1526-41b1-8bef-dd53534c97dfn%40googlegroups.com.

--

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

[Peter Schumann]

Hi Anthony, 

Yep, I was using the "Human_AFFY_HG_U133_MSigDB" chip... probably from looking at the "Diabetes" file listed above the leukemia file... (*sigh*) But thank you very much for your prompt and helpful response! 

Peter

To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/CAGCeyZwo2W30GuT3s7X8wu00o72pFgfV%2BRiSsaqk0AoKB6QTXA%40mail.gmail.com.