GSEA v2.0.4 Release Notes
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Release 2.0.4 significantly increases the processing speed of the algorithm. Our thanks to Justin Guinney of Duke University who submitted this enhancement to the code. There is no change to the GSEA algorithm. This modification simply increases the speed of the Java GSEA application.
Timing data: On Mac OS X version 10.5.4 (2.5 GHz, 4GB RAM), GSEA was launched with 1GB memory. We analyzed the P53_hgu95av2.gct dataset using the full C2 gene set collection and 1000 permutations. Under the previous release, the analysis took 2441 seconds. Under the current release, 662 seconds.