Hi all, I have a question about GSEA analysis. There is an parameter about phenotype label (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!
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