Hi all,

I have a question about GSEA analysis. There is an item about phenotype
lable in Java version GSEA, it is about the .cls data, with an extension,
e.g. "WT~KO", or "KO~"WT". I tried both way, the results are quite
different. The way described in the original paper on how GSEA works does
not seem give an excuse how this parameter affect the results, and why this
happened. Please help!

Wenhuo Hu,
MSKCC

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