GSEA Gene set enrichment analysis portal 09-22-2014d1649

2015-03-10

GSEA Gene set enrichment analysis portal 09-22-2014d1649

Method from the Broad Institute and made freely available (both software and gene set databases)
http://www.broadinstitute.org/gsea/index.jsp

Here's a youtube video (I don't know if it was all that useful)

Gene Set Enrichment Analysis - YouTube (www.youtube.com/watch?v=5Y9rCYldlzo

First encountered in Christian's myocardial infarction paper

cni_Myocardial infarction tert gene therapy project 09-21-2014d1646

Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S. & Mesirov, J. P. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-15550.

paper recommended by Cian pre 10-09-2014d1503
Gene set enrichment analysis A knowledge-based approach for interpreting genome-wide expression profiles

Questions

When deciding whether a gsea is statistically significant, what should be considered: the p-value or the q-value or some other value? 03-10-2015d1147
-I'm quite sure that it is the FDR q-value that should be considered

Some items

the results may have some files with really long filenames, therefore it is probably best to save the output files in a very high up directory (such as C:\Users\kurtw_000\Documents\kurt\storage\long)